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• NJplot
  ...in the [[Newick phylogenetic tree format]] (e.g., the format used by the [[PHYLIP]] package). It was written by M. Gouy.<ref name="Perriere1996">Perrière G, ...ile in the Newick format (i.e., the file format used for trees by Clustal, PHYLIP, and other programs).
  4 KB (587 words) - 02:42, 13 July 2012
• Clustal
  ...ut format can be one or many of the following: Clustal, NBRF/PIR, GCG/MSF, PHYLIP, GDE, NEXUS.
  4 KB (596 words) - 02:18, 13 July 2012
• ClustalW
  ...ld consider removing the most distantly related sequences and/or using the PHYLIP package instead. ...disappear if you run the analysis with a different input order. Again, the PHYLIP package deals with this by offering a JUMBLE option to shuffle the input or
  16 KB (2,365 words) - 20:40, 6 November 2008
• Newick phylogenetic tree format
  * [[PHYLIP]] (Joseph Felsenstein) requires that an unrooted tree begin with a trifurca * [http://evolution.genetics.washington.edu/phylip/newicktree.html The Newick tree format] &mdash; Joseph Felsenstein.
  8 KB (1,220 words) - 02:23, 6 March 2009
• Bioinformatics resource list
  ; PHYLIPNEW : EMBOSS:PHYLIP Applications. (''License: GPL'')
  13 KB (1,598 words) - 06:08, 20 May 2008
• T-Coffee
  ...e to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT
  7 KB (968 words) - 03:25, 22 September 2008
• Bioinformatics
  ...Clustal programs, phylogenetic tree calculation with the [[Clustal]] or [[Phylip]] packages and tree display using [http://www.phylodiversity.net/rree/drawt *Phylogenetic Prediction: CN3D, MMDB, VAST, PREDATOR, Phylip
  5 KB (695 words) - 04:25, 25 April 2007
• Bioinformatics links
  *[http://evolution.genetics.washington.edu/phylip.html PHYLIP] *[http://evolution.genetics.washington.edu/phylip/software.html List]
  16 KB (2,357 words) - 23:50, 20 June 2008
• List of EMBOSS programs
  ...IPNEW programs are EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, version 3.69.
  21 KB (2,762 words) - 01:04, 10 July 2012
• List of SEALS programs
  ;fasta2phylip : convert aligned fasta records to PHYLIP format. ;phylip2fasta : convert PHYLIP alignments to aligned fasta records
  10 KB (1,464 words) - 06:54, 4 May 2007
• Bioinformatics tools
  * [[PHYLIP#ProtPars|ProtPars]] in [[PHYLIP]] * [[PHYLIP#Neighbor|Neighbor]] and [[PHYLIP#ProtDist|ProtDist]] tools in [[PHYLIP]]
  5 KB (588 words) - 22:14, 15 May 2008