Internet Resources

 
Bioinformatics & Genomics


 
Multiple Alignment & Phylogeny



 
Multiple Alignment



 
Phylogeny

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AllAll
[CBRG] Performs a number of different relationships in a set of related peptides.

[more info][10433]

BLOCK
[Aalborg University] This Blocking Gibbs Sampling for Pedigree (Linkage) Analysis in Very Large Pedigrees program is for linkage analysis of large complex pedigrees.



[more info][11151]

GENEHUNTER
[MIT] A software package that allows the very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size. This information is then used in exact computation of multipoint LOD scores and in a new method of non-parametric linkage analysis.



[more info][11162]

Genetic Code Viewer
[EMBL] A tool for browsing different versions of genetic code used by various taxonomic groups.

[more info][10394]

PAML
[Ziheng Yang] A program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood.



[more info][11193]

PASSML
[University of Cambridge] A program for infering phylogeny of globular proteins.


[more info][12184]

PHYLIP Home Page
[University of Washington] (PHYLogeny Inference Package) “PHYLIP is a package of programs for inferring phylogenies. Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters.”

[more info][12180]

PhyloBLAST
[Pathogenomics Project, Univ. British Columbia] Do molecular phylogenetics analysis of a protein sequence. Enter the sequence at the site. PhyloBLAST uses BLASTP to find related amino acid sequences in the Swiss-Prot database. Select those sequences desired, for a full phylogenetic analysis, satrting with a ClustalW multiple sequence alignment. A choice of Phylip programs, including parsimony, UPGMA, neighbor joining and distance matrix methods, produces a phylogenetic tree.

[more info][13729]

Phylogenetics Resources
[University of California at Berkeley] A listing of Phylogenetic resources including societies, publications, databases, and software..

[more info][12183]

Phylogeny Programs
[University of Washington] A list of over 100 phylogeny software packages.





[more info][11375]

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WebPhylip
[National University of Singapore] “WebPHYLIP is a Web version of the original PHYLIP package. Both the original programs and documention
were modified to reflect the WebPHYLIP interface.”

[more info][12187]