`biobox`

Description

Tools for bioinformatics, many of which are also used in the text book Bioinformatics for Evolutionary Biologists by Bernhard Haubold and Angelika Börsch-Haubold.

Bernhard Haubold, haubold@evolbio.mpg.de

Install Windows Subsystem for Linux
Clone repo and install additional packages

git clone https://github.com/evolbioinf/biobox
cd biobox
bash scripts/setup.sh
Make package

make

The directory bin should now contain the programs listed in progs.txt

Install X-Code

xcode-select --install
Install Homebrew
Install packages

brew tap brewsci/bio
brew install brewsci/bio/libdivsufsort git gnuplot golang graphviz gsl tcl-tk xquartz
git clone https://github.com/evolbioinf/biobox
cd biobox
Make package

make

The directory bin should now contain the programs listed in progs.txt

Name		Name	Last commit message	Last commit date
Latest commit History 377 Commits
al		al
blast2dot		blast2dot
bwt		bwt
clac		clac
cres		cres
cutSeq		cutSeq
dnaDist		dnaDist
doc		doc
drag		drag
drawGenes		drawGenes
drawKt		drawKt
drawSt		drawSt
drawf		drawf
fasta2tab		fasta2tab
geco		geco
genTree		genTree
getSeq		getSeq
histogram		histogram
huff		huff
hut		hut
kerror		kerror
keyMat		keyMat
maf		maf
midRoot		midRoot
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
ranDot		ranDot
randomizeSeq		randomizeSeq
ranseq		ranseq
rep2plot		rep2plot
repeater		repeater
revComp		revComp
rpois		rpois
sass		sass
sblast		sblast
scripts		scripts
sequencer		sequencer
shustring		shustring
simNorm		simNorm
simOrf		simOrf
sops		sops
sw		sw
testMeans		testMeans
translate		translate
travTree		travTree
upgma		upgma
util		util
var		var
watterson		watterson
wrapSeq		wrapSeq
.gitignore		.gitignore
Makefile		Makefile
README.md		README.md
go.mod		go.mod
go.sum		go.sum