Bioinformatics Links Directory : Phylogeny Reconstruction

This section contains links to tools and databases for phylogeny reconstruction, including taxonomy resources.

BLASTO - (Found June 29, 2008 )

BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.
http://oxytricha.princeton.edu/BlastO/index.html

PHYML - (Found June 29, 2008 )

Phyml is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method.
http://atgc.lirmm.fr/phyml/

POWER - (Found June 29, 2008 )

The Phylogenetic Web Repeater (POWER) allows users to perform phylogenetic analysis using the PHYLIP package. The POWER pipeline can start with processing either multiple sequence alignments (MSA) or can proceed directly with aligned sequences.
http://power.nhri.org.tw/

Puzzleboot - (Found June 29, 2008 )

Puzzleboot is a UNIX shell script facilitating bootstrap analysis using TREE-PUZZLE and PHYLIP. It enhances TREE-PUZZLE by allowing one to analyse multiple datasets, and can be used for both protein and DNA distance bootstrap analysis.
http://www.tree-puzzle.de/#puzzleboot

Ribosomal Database Project - (Found June 29, 2008 )

Highly curated database of aligned and annotated rRNA sequences with accompanying phylogenies; data available for download.
http://rdp.cme.msu.edu/

Selecton - (Found June 29, 2008 )

Selecton is a server for the identification of site-specific positive selection and purifying selection.
http://selecton.bioinfo.tau.ac.il/

SLAM - (Found June 29, 2008 )

SLAM is a comparative-based annotation and alignment tool for syntenic genomic sequences that performs gene finding and alignment simultaneously. SLAM also predicts CNSs (conserved non-coding sequences).
http://baboon.math.berkeley.edu/~syntenic/slam.html

SPRING - (Found June 29, 2008 )

Sorting Permutation by Reversals and Block Interchanges (SPRING) is a tool for the analysis of genome rearrangements. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals andor block-interchanges for transforming one chromosome into another. Phylogenetic trees based on the rearrangement analysis are also shown as part of the results.
http://algorithm.cs.nthu.edu.tw/tools/SPRING

SWAKK - (Found June 29, 2008 )

Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure.
http://oxytricha.princeton.edu/SWAKK/

Tree Editors - (Found June 29, 2008 )

Tree Editors is an annotated listing of software for the visualization and manipulation of phylogenetic trees.
http://bioinfo.unice.fr/biodiv/Tree_editors.html