Box 355065
Seattle WA 98195
wjs18 (at) u.washington.edu
(206) 221-5124
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| Foege Building Box 355065 Seattle WA 98195 wjs18 (at) u.washington.edu (206) 221-5124 |
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PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood:
Phred/Phrap/Consed is used to make base calls and assemble Chromatograms into reads. Assemblies are visualized using Consed:
PolyPhred is a program that identifies heterozygous sites for single nucleotide substitutions:
MEGA is an integrated tool for automatic and manual sequence alignment,
inferring phylogenetic trees, mining web-based databases, estimating rates
of molecular evolution, and testing evolutionary hypotheses:
Single Likelihood Ancestor Counting (SLAC) analysis , a heavily modified and efficiently implemented version of the Suzuki-Gojobori method (*), to identify positively and negatively selected sites in codon alignments of up to 150 sequences and up to 10000 codons:
HYPHY is a software package intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses: SMART, Simple Modular Architecture Research Tool for visualizing protein structure:
Arlequin is a population genetics software able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing allele frequency data:
Se-Al, manual sequence alignment editor for the
Macintosh:
Other useful sites: |
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