Web Resources on Phylogenetic Tree Reconstruction

Compiled by Graeme Campbell

• 
  
• http://evolution.genetics.washington.edu/phylip/software.html
  -- a list of Phylogeny programs
• ftp://ftp-igbmc.u-strasbg.fr/pub/
  -- ClustalW and ClustalX (for download; now available on crete in the beta-lab in /project/BETA-Bioinf; run "clustalw")
• http://evolution.genetics.washington.edu/phylip.html
  -- Phylip (for download)
• CBR: http://www.cbr.nrc.ca/cgi-bin/WebPhylip/index.html
  Inst. Pasteur: http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html
  -- PHYLIP (web based submission form)
• CBR: http://www.cbr.nrc.ca/newdocs/services/clustalw_form.html
  EBI: http://www2.ebi.ac.uk/clustalw/
  -- ClustalW
• EBI: http://www2.ebi.ac.uk/bic_sw/
  -- Smith-Waterman (full global alignments, more accurate but slow)
• http://www.pathogenomics.bc.ca/phyloBLAST/
  -- PhyloBLAST: allows you to blast a sequence against SWISSPROT/TREMBL databases, then run a phylogenetic analysis.