muscle - amd64

aligngivenpath.cpp

Class

./aligngivenpath.cpp.002t.class

Gimple

./aligngivenpath.cpp.004t.gimple

GKD

./aligngivenpath.o.gkd

OBJ

obj: ./aligngivenpath.o

aligngivenpathsw.cpp

Class

./aligngivenpathsw.cpp.002t.class

Gimple

./aligngivenpathsw.cpp.004t.gimple

GKD

./aligngivenpathsw.o.gkd

OBJ

obj: ./aligngivenpathsw.o

aligntwomsas.cpp

Class

./aligntwomsas.cpp.002t.class

Gimple

./aligntwomsas.cpp.004t.gimple

GKD

./aligntwomsas.o.gkd

OBJ

obj: ./aligntwomsas.o

aligntwoprofs.cpp

Class

./aligntwoprofs.cpp.002t.class

Gimple

./aligntwoprofs.cpp.004t.gimple

GKD

./aligntwoprofs.o.gkd

OBJ

obj: ./aligntwoprofs.o

aln.cpp

Class

./aln.cpp.002t.class

Gimple

./aln.cpp.004t.gimple

GKD

./aln.o.gkd

OBJ

obj: ./aln.o

alpha.cpp

Class

./alpha.cpp.002t.class

Gimple

./alpha.cpp.004t.gimple

GKD

./alpha.o.gkd

OBJ

obj: ./alpha.o

anchors.cpp

Class

./anchors.cpp.002t.class

Gimple

./anchors.cpp.004t.gimple

GKD

./anchors.o.gkd

OBJ

obj: ./anchors.o

bittraceback.cpp

Class

./bittraceback.cpp.002t.class

Gimple

./bittraceback.cpp.004t.gimple

GKD

./bittraceback.o.gkd

OBJ

obj: ./bittraceback.o

unassigned

blosum62.cpp

Class

./blosum62.cpp.002t.class

Gimple

./blosum62.cpp.004t.gimple

GKD

./blosum62.o.gkd

OBJ

obj: ./blosum62.o

unassigned

blosumla.cpp

Class

./blosumla.cpp.002t.class

Gimple

./blosumla.cpp.004t.gimple

GKD

./blosumla.o.gkd

OBJ

obj: ./blosumla.o

clust.cpp

Class

./clust.cpp.002t.class

Gimple

./clust.cpp.004t.gimple

GKD

./clust.o.gkd

OBJ

obj: ./clust.o

cluster.cpp

Class

./cluster.cpp.002t.class

Gimple

./cluster.cpp.004t.gimple

GKD

./cluster.o.gkd

OBJ

obj: ./cluster.o

clwwt.cpp

Class

./clwwt.cpp.002t.class

Gimple

./clwwt.cpp.004t.gimple

GKD

./clwwt.o.gkd

OBJ

obj: ./clwwt.o

color.cpp

Class

./color.cpp.002t.class

Gimple

./color.cpp.004t.gimple

GKD

./color.o.gkd

OBJ

obj: ./color.o

cons.cpp

Class

./cons.cpp.002t.class

Gimple

./cons.cpp.004t.gimple

GKD

./cons.o.gkd

OBJ

obj: ./cons.o

diaglist.cpp

Class

./diaglist.cpp.002t.class

Gimple

./diaglist.cpp.004t.gimple

GKD

./diaglist.o.gkd

OBJ

obj: ./diaglist.o

diffobjscore.cpp

Class

./diffobjscore.cpp.002t.class

Gimple

./diffobjscore.cpp.004t.gimple

GKD

./diffobjscore.o.gkd

OBJ

obj: ./diffobjscore.o

diffpaths.cpp

Class

./diffpaths.cpp.002t.class

Gimple

./diffpaths.cpp.004t.gimple

GKD

./diffpaths.o.gkd

OBJ

obj: ./diffpaths.o

difftrees.cpp

Class

./difftrees.cpp.002t.class

Gimple

./difftrees.cpp.004t.gimple

GKD

./difftrees.o.gkd

OBJ

obj: ./difftrees.o

difftreese.cpp

Class

./difftreese.cpp.002t.class

Gimple

./difftreese.cpp.004t.gimple

GKD

./difftreese.o.gkd

OBJ

obj: ./difftreese.o

distcalc.cpp

Class

./distcalc.cpp.002t.class

Gimple

./distcalc.cpp.004t.gimple

GKD

./distcalc.o.gkd

OBJ

obj: ./distcalc.o

distfunc.cpp

Class

./distfunc.cpp.002t.class

Gimple

./distfunc.cpp.004t.gimple

GKD

./distfunc.o.gkd

OBJ

obj: ./distfunc.o

distpwkimura.cpp

Class

./distpwkimura.cpp.002t.class

Gimple

./distpwkimura.cpp.004t.gimple

GKD

./distpwkimura.o.gkd

OBJ

obj: ./distpwkimura.o

unassigned

domuscle.cpp

Class

./domuscle.cpp.002t.class

Gimple

./domuscle.cpp.004t.gimple

GKD

./domuscle.o.gkd

OBJ

obj: ./domuscle.o

unassigned

dosp.cpp

Class

./dosp.cpp.002t.class

Gimple

./dosp.cpp.004t.gimple

GKD

./dosp.o.gkd

OBJ

obj: ./dosp.o

dpreglist.cpp

Class

./dpreglist.cpp.002t.class

Gimple

./dpreglist.cpp.004t.gimple

GKD

./dpreglist.o.gkd

OBJ

obj: ./dpreglist.o

drawtree.cpp

Class

./drawtree.cpp.002t.class

Gimple

./drawtree.cpp.004t.gimple

GKD

./drawtree.o.gkd

OBJ

obj: ./drawtree.o

edgelist.cpp

Class

./edgelist.cpp.002t.class

Gimple

./edgelist.cpp.004t.gimple

GKD

./edgelist.o.gkd

OBJ

obj: ./edgelist.o

unassigned

unassigned

enumtostr.cpp

Class

./enumtostr.cpp.002t.class

Gimple

./enumtostr.cpp.004t.gimple

GKD

./enumtostr.o.gkd

OBJ

obj: ./enumtostr.o

estring.cpp

Class

./estring.cpp.002t.class

Gimple

./estring.cpp.004t.gimple

GKD

./estring.o.gkd

OBJ

obj: ./estring.o

fasta.cpp

Class

./fasta.cpp.002t.class

Gimple

./fasta.cpp.004t.gimple

GKD

./fasta.o.gkd

OBJ

obj: ./fasta.o

fasta2.cpp

Class

./fasta2.cpp.002t.class

Gimple

./fasta2.cpp.004t.gimple

GKD

./fasta2.o.gkd

OBJ

obj: ./fasta2.o

unassigned

fastclust.cpp

Class

./fastclust.cpp.002t.class

Gimple

./fastclust.cpp.004t.gimple

GKD

./fastclust.o.gkd

OBJ

obj: ./fastclust.o

fastdist.cpp

Class

./fastdist.cpp.002t.class

Gimple

./fastdist.cpp.004t.gimple

GKD

./fastdist.o.gkd

OBJ

obj: ./fastdist.o

fastdistjones.cpp

Class

./fastdistjones.cpp.002t.class

Gimple

./fastdistjones.cpp.004t.gimple

GKD

./fastdistjones.o.gkd

OBJ

obj: ./fastdistjones.o

fastdistkbit.cpp

Class

./fastdistkbit.cpp.002t.class

Gimple

./fastdistkbit.cpp.004t.gimple

GKD

./fastdistkbit.o.gkd

OBJ

obj: ./fastdistkbit.o

fastdistkmer.cpp

Class

./fastdistkmer.cpp.002t.class

Gimple

./fastdistkmer.cpp.004t.gimple

GKD

./fastdistkmer.o.gkd

OBJ

obj: ./fastdistkmer.o

fastdistmafft.cpp

Class

./fastdistmafft.cpp.002t.class

Gimple

./fastdistmafft.cpp.004t.gimple

GKD

./fastdistmafft.o.gkd

OBJ

obj: ./fastdistmafft.o

fastdistnuc.cpp

Class

./fastdistnuc.cpp.002t.class

Gimple

./fastdistnuc.cpp.004t.gimple

GKD

./fastdistnuc.o.gkd

OBJ

obj: ./fastdistnuc.o

fastscorepath2.cpp

Class

./fastscorepath2.cpp.002t.class

Gimple

./fastscorepath2.cpp.004t.gimple

GKD

./fastscorepath2.o.gkd

OBJ

obj: ./fastscorepath2.o

finddiags.cpp

Class

./finddiags.cpp.002t.class

Gimple

./finddiags.cpp.004t.gimple

GKD

./finddiags.o.gkd

OBJ

obj: ./finddiags.o

finddiagsn.cpp

Class

./finddiagsn.cpp.002t.class

Gimple

./finddiagsn.cpp.004t.gimple

GKD

./finddiagsn.o.gkd

OBJ

obj: ./finddiagsn.o

glbalign.cpp

Class

./glbalign.cpp.002t.class

Gimple

./glbalign.cpp.004t.gimple

GKD

./glbalign.o.gkd

OBJ

obj: ./glbalign.o

unassigned

glbaligndiag.cpp

Class

./glbaligndiag.cpp.002t.class

Gimple

./glbaligndiag.cpp.004t.gimple

GKD

./glbaligndiag.o.gkd

OBJ

obj: ./glbaligndiag.o

glbalignle.cpp

Class

./glbalignle.cpp.002t.class

Gimple

./glbalignle.cpp.004t.gimple

GKD

./glbalignle.o.gkd

OBJ

obj: ./glbalignle.o

glbalignsimple.cpp

Class

./glbalignsimple.cpp.002t.class

Gimple

./glbalignsimple.cpp.004t.gimple

GKD

./glbalignsimple.o.gkd

OBJ

obj: ./glbalignsimple.o

glbalignsp.cpp

Class

./glbalignsp.cpp.002t.class

Gimple

./glbalignsp.cpp.004t.gimple

GKD

./glbalignsp.o.gkd

OBJ

obj: ./glbalignsp.o

glbalignspn.cpp

Class

./glbalignspn.cpp.002t.class

Gimple

./glbalignspn.cpp.004t.gimple

GKD

./glbalignspn.o.gkd

OBJ

obj: ./glbalignspn.o

glbalignss.cpp

Class

./glbalignss.cpp.002t.class

Gimple

./glbalignss.cpp.004t.gimple

GKD

./glbalignss.o.gkd

OBJ

obj: ./glbalignss.o

unassigned

glbalndimer.cpp

Class

./glbalndimer.cpp.002t.class

Gimple

./glbalndimer.cpp.004t.gimple

GKD

./glbalndimer.o.gkd

OBJ

obj: ./glbalndimer.o

globals.cpp

Class

./globals.cpp.002t.class

Gimple

./globals.cpp.004t.gimple

GKD

./globals.o.gkd

OBJ

obj: ./globals.o

globalslinux.cpp

Class

./globalslinux.cpp.002t.class

Gimple

./globalslinux.cpp.004t.gimple

GKD

./globalslinux.o.gkd

OBJ

obj: ./globalslinux.o

unassigned

unassigned

gonnet.cpp

Class

./gonnet.cpp.002t.class

Gimple

./gonnet.cpp.004t.gimple

GKD

./gonnet.o.gkd

OBJ

obj: ./gonnet.o

henikoffweight.cpp

Class

./henikoffweight.cpp.002t.class

Gimple

./henikoffweight.cpp.004t.gimple

GKD

./henikoffweight.o.gkd

OBJ

obj: ./henikoffweight.o

henikoffweightpb.cpp

Class

./henikoffweightpb.cpp.002t.class

Gimple

./henikoffweightpb.cpp.004t.gimple

GKD

./henikoffweightpb.o.gkd

OBJ

obj: ./henikoffweightpb.o

html.cpp

Class

./html.cpp.002t.class

Gimple

./html.cpp.004t.gimple

GKD

./html.o.gkd

OBJ

obj: ./html.o

hydro.cpp

Class

./hydro.cpp.002t.class

Gimple

./hydro.cpp.004t.gimple

GKD

./hydro.o.gkd

OBJ

obj: ./hydro.o

intmath.cpp

Class

./intmath.cpp.002t.class

Gimple

./intmath.cpp.004t.gimple

GKD

./intmath.o.gkd

OBJ

obj: ./intmath.o

local.cpp

Class

./local.cpp.002t.class

Gimple

./local.cpp.004t.gimple

GKD

./local.o.gkd

OBJ

obj: ./local.o

main.cpp

Class

./main.cpp.002t.class

Gimple

./main.cpp.004t.gimple

GKD

./main.o.gkd

OBJ

obj: ./main.o

unassigned

makerootmsa.cpp

Class

./makerootmsa.cpp.002t.class

Gimple

./makerootmsa.cpp.004t.gimple

GKD

./makerootmsa.o.gkd

OBJ

obj: ./makerootmsa.o

makerootmsab.cpp

Class

./makerootmsab.cpp.002t.class

Gimple

./makerootmsab.cpp.004t.gimple

GKD

./makerootmsab.o.gkd

OBJ

obj: ./makerootmsab.o

unassigned

maketree.cpp

Class

./maketree.cpp.002t.class

Gimple

./maketree.cpp.004t.gimple

GKD

./maketree.o.gkd

OBJ

obj: ./maketree.o

mhack.cpp

Class

./mhack.cpp.002t.class

Gimple

./mhack.cpp.004t.gimple

GKD

./mhack.o.gkd

OBJ

obj: ./mhack.o

unassigned

mpam200.cpp

Class

./mpam200.cpp.002t.class

Gimple

./mpam200.cpp.004t.gimple

GKD

./mpam200.o.gkd

OBJ

obj: ./mpam200.o

unassigned

msa.cpp

Class

./msa.cpp.002t.class

Gimple

./msa.cpp.004t.gimple

GKD

./msa.o.gkd

OBJ

obj: ./msa.o

unassigned

msa2.cpp

Class

./msa2.cpp.002t.class

Gimple

./msa2.cpp.004t.gimple

GKD

./msa2.o.gkd

OBJ

obj: ./msa2.o

msadistkimura.cpp

Class

./msadistkimura.cpp.002t.class

Gimple

./msadistkimura.cpp.004t.gimple

GKD

./msadistkimura.o.gkd

OBJ

obj: ./msadistkimura.o

msf.cpp

Class

./msf.cpp.002t.class

Gimple

./msf.cpp.004t.gimple

GKD

./msf.o.gkd

OBJ

obj: ./msf.o

unassigned

muscle.cpp

Class

./muscle.cpp.002t.class

Gimple

./muscle.cpp.004t.gimple

GKD

./muscle.o.gkd

OBJ

obj: ./muscle.o

muscleout.cpp

Class

./muscleout.cpp.002t.class

Gimple

./muscleout.cpp.004t.gimple

GKD

./muscleout.o.gkd

OBJ

obj: ./muscleout.o

unassigned

nucmx.cpp

Class

./nucmx.cpp.002t.class

Gimple

./nucmx.cpp.004t.gimple

GKD

./nucmx.o.gkd

OBJ

obj: ./nucmx.o

unassigned

nwdasimple.cpp

Class

./nwdasimple.cpp.002t.class

Gimple

./nwdasimple.cpp.004t.gimple

GKD

./nwdasimple.o.gkd

OBJ

obj: ./nwdasimple.o

unassigned

unassigned

nwsmall.cpp

Class

./nwsmall.cpp.002t.class

Gimple

./nwsmall.cpp.004t.gimple

GKD

./nwsmall.o.gkd

OBJ

obj: ./nwsmall.o

objscore.cpp

Class

./objscore.cpp.002t.class

Gimple

./objscore.cpp.004t.gimple

GKD

./objscore.o.gkd

OBJ

obj: ./objscore.o

objscore2.cpp

Class

./objscore2.cpp.002t.class

Gimple

./objscore2.cpp.004t.gimple

GKD

./objscore2.o.gkd

OBJ

obj: ./objscore2.o

unassigned

onexception.cpp

Class

./onexception.cpp.002t.class

Gimple

./onexception.cpp.004t.gimple

GKD

./onexception.o.gkd

OBJ

obj: ./onexception.o

options.cpp

Class

./options.cpp.002t.class

Gimple

./options.cpp.004t.gimple

GKD

./options.o.gkd

OBJ

obj: ./options.o

outweights.cpp

Class

./outweights.cpp.002t.class

Gimple

./outweights.cpp.004t.gimple

GKD

./outweights.o.gkd

OBJ

obj: ./outweights.o

unassigned

pam200mafft.cpp

Class

./pam200mafft.cpp.002t.class

Gimple

./pam200mafft.cpp.004t.gimple

GKD

./pam200mafft.o.gkd

OBJ

obj: ./pam200mafft.o

params.cpp

Class

./params.cpp.002t.class

Gimple

./params.cpp.004t.gimple

GKD

./params.o.gkd

OBJ

obj: ./params.o

phy.cpp

Class

./phy.cpp.002t.class

Gimple

./phy.cpp.004t.gimple

GKD

./phy.o.gkd

OBJ

obj: ./phy.o

phy2.cpp

Class

./phy2.cpp.002t.class

Gimple

./phy2.cpp.004t.gimple

GKD

./phy2.o.gkd

OBJ

obj: ./phy2.o

phy3.cpp

Class

./phy3.cpp.002t.class

Gimple

./phy3.cpp.004t.gimple

GKD

./phy3.o.gkd

OBJ

obj: ./phy3.o

phy4.cpp

Class

./phy4.cpp.002t.class

Gimple

./phy4.cpp.004t.gimple

GKD

./phy4.o.gkd

OBJ

obj: ./phy4.o

phyfromclust.cpp

Class

./phyfromclust.cpp.002t.class

Gimple

./phyfromclust.cpp.004t.gimple

GKD

./phyfromclust.o.gkd

OBJ

obj: ./phyfromclust.o

phyfromfile.cpp

Class

./phyfromfile.cpp.002t.class

Gimple

./phyfromfile.cpp.004t.gimple

GKD

./phyfromfile.o.gkd

OBJ

obj: ./phyfromfile.o

physeq.cpp

Class

./physeq.cpp.002t.class

Gimple

./physeq.cpp.004t.gimple

GKD

./physeq.o.gkd

OBJ

obj: ./physeq.o

phytofile.cpp

Class

./phytofile.cpp.002t.class

Gimple

./phytofile.cpp.004t.gimple

GKD

./phytofile.o.gkd

OBJ

obj: ./phytofile.o

posgap.cpp

Class

./posgap.cpp.002t.class

Gimple

./posgap.cpp.004t.gimple

GKD

./posgap.o.gkd

OBJ

obj: ./posgap.o

ppscore.cpp

Class

./ppscore.cpp.002t.class

Gimple

./ppscore.cpp.004t.gimple

GKD

./ppscore.o.gkd

OBJ

obj: ./ppscore.o

profdb.cpp

Class

./profdb.cpp.002t.class

Gimple

./profdb.cpp.004t.gimple

GKD

./profdb.o.gkd

OBJ

obj: ./profdb.o

profile.cpp

Class

./profile.cpp.002t.class

Gimple

./profile.cpp.004t.gimple

GKD

./profile.o.gkd

OBJ

obj: ./profile.o

profilefrommsa.cpp

Class

./profilefrommsa.cpp.002t.class

Gimple

./profilefrommsa.cpp.004t.gimple

GKD

./profilefrommsa.o.gkd

OBJ

obj: ./profilefrommsa.o

progalign.cpp

Class

./progalign.cpp.002t.class

Gimple

./progalign.cpp.004t.gimple

GKD

./progalign.o.gkd

OBJ

obj: ./progalign.o

progress.cpp

Class

./progress.cpp.002t.class

Gimple

./progress.cpp.004t.gimple

GKD

./progress.o.gkd

OBJ

obj: ./progress.o

progressivealign.cpp

Class

./progressivealign.cpp.002t.class

Gimple

./progressivealign.cpp.004t.gimple

GKD

./progressivealign.o.gkd

OBJ

obj: ./progressivealign.o

pwpath.cpp

Class

./pwpath.cpp.002t.class

Gimple

./pwpath.cpp.004t.gimple

GKD

./pwpath.o.gkd

OBJ

obj: ./pwpath.o

readmx.cpp

Class

./readmx.cpp.002t.class

Gimple

./readmx.cpp.004t.gimple

GKD

./readmx.o.gkd

OBJ

obj: ./readmx.o

realigndiffs.cpp

Class

./realigndiffs.cpp.002t.class

Gimple

./realigndiffs.cpp.004t.gimple

GKD

./realigndiffs.o.gkd

OBJ

obj: ./realigndiffs.o

realigndiffse.cpp

Class

./realigndiffse.cpp.002t.class

Gimple

./realigndiffse.cpp.004t.gimple

GKD

./realigndiffse.o.gkd

OBJ

obj: ./realigndiffse.o

unassigned

refine.cpp

Class

./refine.cpp.002t.class

Gimple

./refine.cpp.004t.gimple

GKD

./refine.o.gkd

OBJ

obj: ./refine.o

refinehoriz.cpp

Class

./refinehoriz.cpp.002t.class

Gimple

./refinehoriz.cpp.004t.gimple

GKD

./refinehoriz.o.gkd

OBJ

obj: ./refinehoriz.o

unassigned

refinesubfams.cpp

Class

./refinesubfams.cpp.002t.class

Gimple

./refinesubfams.cpp.004t.gimple

GKD

./refinesubfams.o.gkd

OBJ

obj: ./refinesubfams.o

unassigned

refinetree.cpp

Class

./refinetree.cpp.002t.class

Gimple

./refinetree.cpp.004t.gimple

GKD

./refinetree.o.gkd

OBJ

obj: ./refinetree.o

unassigned

refinetreee.cpp

Class

./refinetreee.cpp.002t.class

Gimple

./refinetreee.cpp.004t.gimple

GKD

./refinetreee.o.gkd

OBJ

obj: ./refinetreee.o

refinevert.cpp

Class

./refinevert.cpp.002t.class

Gimple

./refinevert.cpp.004t.gimple

GKD

./refinevert.o.gkd

OBJ

obj: ./refinevert.o

unassigned

refinew.cpp

Class

./refinew.cpp.002t.class

Gimple

./refinew.cpp.004t.gimple

GKD

./refinew.o.gkd

OBJ

obj: ./refinew.o

savebest.cpp

Class

./savebest.cpp.002t.class

Gimple

./savebest.cpp.004t.gimple

GKD

./savebest.o.gkd

OBJ

obj: ./savebest.o

scoredist.cpp

Class

./scoredist.cpp.002t.class

Gimple

./scoredist.cpp.004t.gimple

GKD

./scoredist.o.gkd

OBJ

obj: ./scoredist.o

scoregaps.cpp

Class

./scoregaps.cpp.002t.class

Gimple

./scoregaps.cpp.004t.gimple

GKD

./scoregaps.o.gkd

OBJ

obj: ./scoregaps.o

scorehistory.cpp

Class

./scorehistory.cpp.002t.class

Gimple

./scorehistory.cpp.004t.gimple

GKD

./scorehistory.o.gkd

OBJ

obj: ./scorehistory.o

scorepp.cpp

Class

./scorepp.cpp.002t.class

Gimple

./scorepp.cpp.004t.gimple

GKD

./scorepp.o.gkd

OBJ

obj: ./scorepp.o

seq.cpp

Class

./seq.cpp.002t.class

Gimple

./seq.cpp.004t.gimple

GKD

./seq.o.gkd

OBJ

obj: ./seq.o

unassigned

seqvect.cpp

Class

./seqvect.cpp.002t.class

Gimple

./seqvect.cpp.004t.gimple

GKD

./seqvect.o.gkd

OBJ

obj: ./seqvect.o

setblosumweights.cpp

Class

./setblosumweights.cpp.002t.class

Gimple

./setblosumweights.cpp.004t.gimple

GKD

./setblosumweights.o.gkd

OBJ

obj: ./setblosumweights.o

setgscweights.cpp

Class

./setgscweights.cpp.002t.class

Gimple

./setgscweights.cpp.004t.gimple

GKD

./setgscweights.o.gkd

OBJ

obj: ./setgscweights.o

setnewhandler.cpp

Class

./setnewhandler.cpp.002t.class

Gimple

./setnewhandler.cpp.004t.gimple

GKD

./setnewhandler.o.gkd

OBJ

obj: ./setnewhandler.o

spfast.cpp

Class

./spfast.cpp.002t.class

Gimple

./spfast.cpp.004t.gimple

GKD

./spfast.o.gkd

OBJ

obj: ./spfast.o

sptest.cpp

Class

./sptest.cpp.002t.class

Gimple

./sptest.cpp.004t.gimple

GKD

./sptest.o.gkd

OBJ

obj: ./sptest.o

stabilize.cpp

Class

./stabilize.cpp.002t.class

Gimple

./stabilize.cpp.004t.gimple

GKD

./stabilize.o.gkd

OBJ

obj: ./stabilize.o

subfam.cpp

Class

./subfam.cpp.002t.class

Gimple

./subfam.cpp.004t.gimple

GKD

./subfam.o.gkd

OBJ

obj: ./subfam.o

subfams.cpp

Class

./subfams.cpp.002t.class

Gimple

./subfams.cpp.004t.gimple

GKD

./subfams.o.gkd

OBJ

obj: ./subfams.o

sw.cpp

Class

./sw.cpp.002t.class

Gimple

./sw.cpp.004t.gimple

GKD

./sw.o.gkd

OBJ

obj: ./sw.o

termgaps.cpp

Class

./termgaps.cpp.002t.class

Gimple

./termgaps.cpp.004t.gimple

GKD

./termgaps.o.gkd

OBJ

obj: ./termgaps.o

textfile.cpp

Class

./textfile.cpp.002t.class

Gimple

./textfile.cpp.004t.gimple

GKD

./textfile.o.gkd

OBJ

obj: ./textfile.o

threewaywt.cpp

Class

./threewaywt.cpp.002t.class

Gimple

./threewaywt.cpp.004t.gimple

GKD

./threewaywt.o.gkd

OBJ

obj: ./threewaywt.o

tomhydro.cpp

Class

./tomhydro.cpp.002t.class

Gimple

./tomhydro.cpp.004t.gimple

GKD

./tomhydro.o.gkd

OBJ

obj: ./tomhydro.o

traceback.cpp

Class

./traceback.cpp.002t.class

Gimple

./traceback.cpp.004t.gimple

GKD

./traceback.o.gkd

OBJ

obj: ./traceback.o

tracebackopt.cpp

Class

./tracebackopt.cpp.002t.class

Gimple

./tracebackopt.cpp.004t.gimple

GKD

./tracebackopt.o.gkd

OBJ

obj: ./tracebackopt.o

tracebacksw.cpp

Class

./tracebacksw.cpp.002t.class

Gimple

./tracebacksw.cpp.004t.gimple

GKD

./tracebacksw.o.gkd

OBJ

obj: ./tracebacksw.o

unassigned

treefrommsa.cpp

Class

./treefrommsa.cpp.002t.class

Gimple

./treefrommsa.cpp.004t.gimple

GKD

./treefrommsa.o.gkd

OBJ

obj: ./treefrommsa.o

typetostr.cpp

Class

./typetostr.cpp.002t.class

Gimple

./typetostr.cpp.004t.gimple

GKD

./typetostr.o.gkd

OBJ

obj: ./typetostr.o

upgma2.cpp

Class

./upgma2.cpp.002t.class

Gimple

./upgma2.cpp.004t.gimple

GKD

./upgma2.o.gkd

OBJ

obj: ./upgma2.o

usage.cpp

Class

./usage.cpp.002t.class

Gimple

./usage.cpp.004t.gimple

GKD

./usage.o.gkd

OBJ

obj: ./usage.o

unassigned

unassigned

vtml2.cpp

Class

./vtml2.cpp.002t.class

Gimple

./vtml2.cpp.004t.gimple

GKD

./vtml2.o.gkd

OBJ

obj: ./vtml2.o

writescorefile.cpp

Class

./writescorefile.cpp.002t.class

Gimple

./writescorefile.cpp.004t.gimple

GKD

./writescorefile.o.gkd

OBJ

obj: ./writescorefile.o

includes

aligngivenpath.cpp

./msa.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./types.h ./intmath.h ./pwpath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h

aligngivenpathsw.cpp

./msa.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./profile.h

aligntwomsas.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h ./textfile.h

aligntwoprofs.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h

aln.cpp

../headers//usr/include/string.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/ctype.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ./textfile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./enums.h

alpha.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/ctype.h ../headers//usr/include/string.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./alpha.h ../headers//usr/include/stdio.h ./params.h ./muscle.h ./enums.h

anchors.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./objscore.h

bittraceback.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./types.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

blosum62.cpp

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

blosumla.cpp

clust.cpp

./clust.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h

cluster.cpp

./cluster.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./distfunc.h

clwwt.cpp

./tree.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

color.cpp

../headers//usr/include/ctype.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

cons.cpp

../headers//usr/include/ctype.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

diaglist.cpp

./diaglist.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h

diffobjscore.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./types.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./profile.h ./objscore.h

diffpaths.cpp

./pwpath.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

difftrees.cpp

./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

difftreese.cpp

./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

distcalc.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./distcalc.h ./msa.h ./distfunc.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./enums.h

distfunc.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./distfunc.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/stdlib.h ../headers//usr/include/assert.h

distpwkimura.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./seq.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./enums.h

unassigned

./tree.h

domuscle.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./types.h ./enums.h ./intmath.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./seq.h ./profile.h ./msa.h ./alpha.h ./params.h ./muscle.h ./textfile.h ../headers//usr/include/stdlib.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/string.h

unassigned

./tree.h

dosp.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./msa.h ./alpha.h ./params.h ./muscle.h ./textfile.h ./profile.h ./objscore.h ../headers//usr/include/stdlib.h

dpreglist.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./diaglist.h ./dpreglist.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h

drawtree.cpp

./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

edgelist.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./edgelist.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./enumopts.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

unassigned

./enums.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

enumtostr.cpp

../headers//usr/include/string.h

estring.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ./msa.h ./seq.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/stdlib.h

fasta.cpp

./msa.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ./textfile.h ./alpha.h ./muscle.h

fasta2.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/ctype.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ./alpha.h ./muscle.h ../headers//usr/include/x86_64-linux-gnu/bits/errno.h ../headers//usr/include/string.h

unassigned

./clustsetdf.h

fastclust.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ./seqvect.h ./distcalc.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./seq.h ./tree.h ./clust.h ./clustset.h ./distfunc.h ./alpha.h ./muscle.h ./msa.h

fastdist.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ./seq.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./distfunc.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./enums.h

fastdistjones.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ./seq.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/stdlib.h ../headers//usr/include/c++/4.9/new

fastdistkbit.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ./seq.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./types.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./seqvect.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/c++/4.9/new

fastdistkmer.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ./seq.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./types.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h ../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h ../headers//usr/include/c++/4.9/new

fastdistmafft.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ./seq.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h

fastdistnuc.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ./seq.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/c++/4.9/new ./enums.h

fastscorepath2.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h

finddiags.cpp

./diaglist.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ./enums.h

finddiagsn.cpp

./diaglist.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ./enums.h

glbalign.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./textfile.h ./msa.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./textfile.h ./msa.h ./profile.h

glbaligndiag.cpp

./diaglist.h ./dpreglist.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ./enums.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h

glbalignle.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h

glbalignsimple.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h

glbalignsp.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h

glbalignspn.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ./enums.h

glbalignss.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seq.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./types.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ./profile.h ../headers//usr/include/c++/4.9/new

unassigned

./gapscoredimer.h

glbalndimer.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h ./enums.h

globals.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/ctype.h ../headers//usr/include/string.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/time.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./types.h ./enums.h ./intmath.h ./alpha.h ./muscle.h ../headers//usr/include/assert.h ../headers//usr/include/stdlib.h

globalslinux.cpp

../headers//usr/include/x86_64-linux-gnu/bits/fcntl2.h ../headers//usr/include/x86_64-linux-gnu/bits/unistd.h ../headers//usr/include/stdlib.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/string.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/sys/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/unistd.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/x86_64-linux-gnu/bits/errno.h ../headers//usr/include/x86_64-linux-gnu/bits/confname.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

gonnet.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

henikoffweight.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

henikoffweightpb.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

html.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/string.h ../headers//usr/include/ctype.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ./textfile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

hydro.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ./enums.h

intmath.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h

local.cpp

./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./profile.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./textfile.h ../headers//usr/include/stdlib.h

main.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ../headers//usr/include/unistd.h ./types.h ../headers//usr/include/x86_64-linux-gnu/bits/confname.h ../headers//usr/include/stdlib.h

unassigned

./seq.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

makerootmsa.cpp

./seqvect.h ../headers//usr/include/c++/4.9/bits/vector.tcc ./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./profile.h ./msa.h ./pwpath.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ../headers//usr/include/c++/4.9/new ./estring.h

makerootmsab.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ./seq.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ./tree.h ./profile.h ./msa.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/c++/4.9/new

unassigned

./tree.h

maketree.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./textfile.h ../headers//usr/include/stdlib.h

mhack.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ./seq.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/c++/4.9/new ./enums.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

mpam200.cpp

unassigned

./seq.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

msa.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/ctype.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ./msa.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./textfile.h ../headers//usr/include/string.h ./enums.h

unassigned

./seq.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

msa2.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/c++/4.9/bits/vector.tcc ./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./alpha.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./msa.h ./seqvect.h ../headers//usr/include/stdio.h ./muscle.h ./profile.h ../headers//usr/include/c++/4.9/new

msadistkimura.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h ../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h

msf.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ./textfile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./enums.h ../headers//usr/include/string.h

unassigned

./tree.h

muscle.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ./profile.h ./msa.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./seq.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/stdlib.h

muscleout.cpp

./textfile.h ./msa.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ./alpha.h ./params.h ./muscle.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

nucmx.cpp

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h ./profile.h

nwdasimple.cpp

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h ./profile.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h ./profile.h

nwsmall.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ./types.h

objscore.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ./profile.h ./objscore.h ./enums.h

objscore2.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./types.h ./enums.h ./intmath.h ./profile.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h ./profile.h

onexception.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ./alpha.h ./muscle.h ./types.h ../headers//usr/include/stdlib.h

options.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/include/ctype.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ./alpha.h ./muscle.h ../headers//usr/include/string.h ./types.h ../headers//usr/include/stdlib.h

outweights.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ./alpha.h ./muscle.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

pam200mafft.cpp

params.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/stdlib.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./types.h ./enums.h ./intmath.h ./enumopts.h ./muscle.h ../headers//usr/include/stdio.h ./alpha.h ./msa.h ./profile.h ../headers//usr/include/string.h

phy.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/stdlib.h ../headers//usr/include/string.h

phy2.cpp

./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

phy3.cpp

./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ./edgelist.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

phy4.cpp

./tree.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/stdlib.h

phyfromclust.cpp

./tree.h ./clust.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/stdlib.h

phyfromfile.cpp

../headers//usr/include/string.h ../headers//usr/include/ctype.h ./textfile.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ./tree.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/stdlib.h

physeq.cpp

../headers//usr/include/ctype.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ./textfile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/string.h

phytofile.cpp

./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ./textfile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

posgap.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./enums.h

ppscore.cpp

./tree.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./profile.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./textfile.h ./objscore.h ../headers//usr/include/stdlib.h

profdb.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ./seq.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./textfile.h ./tree.h ./clust.h ./profile.h ./enums.h

profile.cpp

./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./profile.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./textfile.h ../headers//usr/include/stdlib.h

profilefrommsa.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./types.h ./intmath.h ./profile.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./enums.h

progalign.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ./profile.h ./tree.h ./msa.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./seq.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./textfile.h ../headers//usr/include/c++/4.9/new

progress.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/time.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ./alpha.h ./params.h ./muscle.h ./types.h

progressivealign.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ./profile.h ./tree.h ./msa.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./seq.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/c++/4.9/new

pwpath.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/stdlib.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./textfile.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/c++/4.9/new

readmx.cpp

../headers//usr/include/ctype.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./types.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./textfile.h ../headers//usr/include/stdlib.h

realigndiffs.cpp

./profile.h ./tree.h ./msa.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

realigndiffse.cpp

./profile.h ./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ../headers//usr/include/c++/4.9/new

unassigned

./tree.h

refine.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./textfile.h ./clust.h ./profile.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/stdlib.h

refinehoriz.cpp

./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ./msa.h ./pwpath.h ./scorehistory.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./profile.h ./objscore.h

unassigned

./tree.h

refinesubfams.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./clust.h ./profile.h ../headers//usr/include/stdlib.h

unassigned

./tree.h

refinetree.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./profile.h ../headers//usr/include/stdlib.h

unassigned

./tree.h

refinetreee.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./profile.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ../headers//usr/include/stdlib.h

refinevert.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./enums.h ./tree.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./profile.h ./clust.h ../headers//usr/include/c++/4.9/new

unassigned

./seq.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

refinew.cpp

../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ./seqvect.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ./msa.h ../headers//usr/include/c++/4.9/new ./alpha.h ./params.h ./muscle.h ./textfile.h

savebest.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/time.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ./alpha.h ./params.h ./muscle.h ./textfile.h ./types.h ../headers//usr/include/stdlib.h

scoredist.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./seq.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h

scoregaps.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./objscore.h

scorehistory.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./scorehistory.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

scorepp.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h ./enums.h

seq.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./seq.h ./msa.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/ctype.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./textfile.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/string.h

unassigned

./seq.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

seqvect.cpp

./seqvect.h ./msa.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ./textfile.h ../headers//usr/include/c++/4.9/new ./alpha.h ./muscle.h ../headers//usr/include/string.h ./enums.h

setblosumweights.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./cluster.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./distfunc.h

setgscweights.cpp

./cluster.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

setnewhandler.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/c++/4.9/new ./alpha.h ./muscle.h ../headers//usr/include/stdlib.h ./types.h

spfast.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./types.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./profile.h

sptest.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ./pwpath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./textfile.h ./objscore.h ./enums.h ../headers//usr/include/stdlib.h

stabilize.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

subfam.cpp

./tree.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./seqvect.h ./textfile.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ./profile.h ./msa.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./types.h ./enums.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ./seq.h ./alpha.h ./params.h ./muscle.h ../headers//usr/include/stdlib.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/unistd.h ../headers//usr/include/string.h

subfams.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

sw.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h

termgaps.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ./msa.h ./enums.h

textfile.cpp

../headers//usr/include/x86_64-linux-gnu/bits/string3.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/include/ctype.h ../headers//usr/include/string.h ./textfile.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ./alpha.h ./muscle.h ../headers//usr/include/x86_64-linux-gnu/bits/errno.h ../headers//usr/include/stdlib.h

threewaywt.cpp

./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./enums.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h

tomhydro.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h ./enums.h

traceback.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h

tracebackopt.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

tracebacksw.cpp

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ./pwpath.h ./profile.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h

unassigned

./clustsetmsa.h ./msadist.h

treefrommsa.cpp

./distcalc.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./tree.h ./msa.h ./clustset.h ./clust.h ./alpha.h ./muscle.h ../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h

typetostr.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

upgma2.cpp

./tree.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./enums.h ./intmath.h ./distcalc.h ../headers//usr/include/stdio.h ./alpha.h ./params.h ./muscle.h ../headers//usr/include/stdlib.h

usage.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ./muscle.h ./alpha.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h ./msa.h ./tree.h

unassigned

../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/libio.h ./intmath.h ../headers//usr/include/stdio.h ./alpha.h ./muscle.h

vtml2.cpp

writescorefile.cpp

../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/x86_64-linux-gnu/bits/types.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ./intmath.h ./msa.h ./alpha.h ./params.h ./muscle.h ./enums.h ../headers//usr/include/x86_64-linux-gnu/bits/errno.h