.gitignore

progs.txt
bin/*
doc/*~
doc/biobox.aux
doc/biobox.bbl
doc/biobox.blg
doc/biobox.dvi
doc/*.log
doc/biobox.pdf
doc/biobox.toc
doc/biobox.ps
doc/date.txt
doc/rd*.ps
doc/version.txt

# LaTeX files of individual programs
doc/al.tex
doc/blast2dot.tex
doc/bwt.tex
doc/clac.tex
doc/cres.tex
doc/cutSeq.tex
doc/dnaDist.tex
doc/drag.tex
doc/drawf.tex
doc/drawGenes.tex
doc/drawKt.tex
doc/drawSt.tex
doc/fasta2tab.tex
doc/geco.tex
doc/genTree.tex
doc/getSeq.tex
doc/histogram.tex
doc/huff.tex
doc/hut.tex
doc/kerror.tex
doc/keyMat.tex
doc/midRoot.tex
doc/maf.tex
doc/mtf.tex
doc/mum2plot.tex
doc/mutator.tex
doc/naiveMatcher.tex
doc/nj.tex
doc/num2char.tex
doc/numAl.tex
doc/olga.tex
doc/pam.tex
doc/plotLine.tex
doc/plotSeg.tex
doc/plotTree.tex
doc/pps.tex
doc/randomizeSeq.tex
doc/ranDot.tex
doc/ranseq.tex
doc/rep2plot.tex
doc/repeater.tex
doc/revComp.tex
doc/rpois.tex
doc/sass.tex
doc/sblast.tex
doc/sequencer.tex
doc/shustring.tex
doc/simNorm.tex
doc/simOrf.tex
doc/sops.tex
doc/sw.tex
doc/testMeans.tex
doc/translate.tex
doc/travTree.tex
doc/util.tex
doc/upgma.tex
doc/var.tex
doc/watterson.tex
doc/wrapSeq.tex

# Programs
al/al
blast2dot/blast2dot
bwt/bwt
clac/clac
cres/cres
cutSeq/cutSeq
dnaDist/dnaDist
drag/drag
drawf/drawf
drawGenes/drawGenes
drawKt/drawKt
drawSt/drawSt
fasta2tab/fasta2tab
geco/geco
genTree/genTree
getSeq/getSeq
histogram/histogram
huff/huff
hut/hut
kerror/kerror
keyMat/keyMat
midRoot/midRoot
maf/maf
mtf/mtf
mum2plot/mum2plot
mutator/mutator
naiveMatcher/naiveMatcher
nj/nj
num2char/num2char
numAl/numAl
olga/olga
pam/pam
plotLine/plotLine
plotSeg/plotSeg
plotTree/plotTree
pps/pps
randomizeSeq/randomizeSeq
ranDot/ranDot
ranseq/ranseq
rep2plot/rep2plot
repeater/repeater
revComp/revComp
rpois/rpois
sass/sass
sblast/sblast
sequencer/sequencer
shustring/shustring
simNorm/simNorm
simOrf/simOrf
sops/sops
sw/sw
testMeans/testMeans
translate/translate
travTree/travTree
upgma/upgma
var/var
watterson/watterson
wrapSeq/wrapSeq

# Miscellaneous
clac/drawTrees.sh
drag/*.awk
drag/*.sh
drawKt/kt.tex
drawKt/ktWrapper*
genTree/makeTests.sh
keyMat/makeRes.sh
plotLine/lineTmpl.txt
plotLine/makeRes.sh
plotSeg/makeRes.sh
plotTree/makePlots.sh
release
ranDot/*.sh
sequencer/makeRes.sh
sw/makeRes.sh