SOFTWARE SOURCES

Programs needed for the Stats workshop at MSA 2009 meeting. 

R:  http://www.r-project.org/
EstimateS:   http://viceroy.eeb.uconn.edu/estimates
Phylocom:   http://www.phylodiversity.net/phylocom/
UniFrac:  http://bmf2.colorado.edu/unifrac/index.psp Web Interface only

 

SEQUENCE ALIGNMENT/PHYLOGENETICS

MUSCLE - Automated Sequence Alignment Tool http://www.drive5.com/muscle/

SATé - Simultaneous Alignment and Tree Estimation http://phylo.bio.ku.edu/software/sate/sate.html

TCS: Phylogenetic network estimation using statistical parsimony    http://darwin.uvigo.es/software/tcs.html

SeAl http://tree.bio.ed.ac.uk/software/seal/

BioEdit www.mbio.ncsu.edu/BioEdit/bioedit.html

TextWrangler http://www.barebones.com/products/textwrangler/

FORMAT CONVERSION

http://hcv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html

TRIM SEQUENCES

http://imed.med.ucm.es/cgi-bin/emboss.pl?_action=input&_app=trimseq

PARSE BLAST OUTPUT

http://157.86.176.108/~catanho/bioparser-web/