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741. PAUP
Software package for inference of evolutionary trees (command paup)
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742. pedcheck
Program for detecting marker typing incompatibilities in pedigree data
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743. Pftools
Profile analysis package providing a very sensitive method for the discovery of distant sequence relationships. Includes pfsearch, pfscan and gtop
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744. phase
A Bayesian statistical method for reconstructing haplotypes from population genotype data
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745. phrap
An assembly program for shotgun DNA sequences. Comes with crossmatch and swat sequence comparison programs. Phrap fait partie de l'ensemble Phred-Phrap-Consed couramment utilisé pour l'assemblage des séquences. Phrap (Phragment Assembly Program) est un programme qui permet l'assemblage...
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746. Phylip
Phylogenetic analysis package with many programs
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747. phyml
Software implementing a method for building phylogenies from DNA and protein sequences using maximum likelihood. Command phyml PhyML [1] is a software package which primary task that is to estimate maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It...
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748. Phylobayes
A Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers (e.g. MrBayes), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. CAT is a mixture model espe...
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749. Picante
Picante is an R package for integrating phylogenies and ecology.
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750. plink
A whole genome association analysis toolset
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751. Picard tools
Java-based tools for manipulating SAM files.
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752. PolyPhred
Package for identifiying SNPS. Used with phred, phrap and consed; commands polyphred and sudophred.
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753. primer3_core
Primer design program
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754. probcons
Program for multiple alignment of protein sequences
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755. ProtTest
Program to select the best-fit model of protein evolution (sibling program to jmodeltest for DNA). Command runProtTest for commandline or runXProtTest for XWindows.
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756. psipred
Protein secondary structure prediction using command runpsipred
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757. pymol
Molecular visualization program
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758. quicktree
Program for the rapid reconstruction of phylogenies by the Neighbor-Joining method QuickTree allows the reconstruction of phylogenies for very large protein families that would be infeasible using other popular methods.
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759. R
The R language and a large number of statistical genetics packages that run in R are available, including Rmpi
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760. rasmol
Molecular viewing program also available for a range of other platforms.
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