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Internet Links for Biogeography, Ecology & Conservation

Joel recommends the following software:

Arlequin - haploid or diploid data as frequencies or sequences, compares localities for nucleotide & haplotype diversities, compares/contrasts localities for F-statistics (evidence of inbreeding or gene flow).
Bottleneck - detects recent effective population size reductions from allele frequency data.
MEGA - excellent alignment checker, also builds phylogenetic trees.
Migrate - part of the Lamarc package, estimates effective pop size and migration rates.
ModelTest - operates with Paup* or MrBayes (depending on version) to check how mutations are accumulating in sequence data.
MrBayes - THE program to construct Bayesian phylogenies with, works inside Paup*.
Paup* - THE program for distance, cladistic, or likelihood phylogeny building. Mac version easily navigated. Purchase required.
Protein Explorer
TreeDyn - very unuser freindly, but the MOST options for tree drawing (converting simpletext trees to colorful, labelled jpegs).
TreePuzzle - phylogeny building with likelihood methods.
TreeView - simple, efficient method of converting most tree output files into bitmap pictures.