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Showing 11 records out of 11 total

Categories: evolutionary biology - Software type(s): website - tool
Neighbor Joining (NJ) algorithm improved for molecular sequences
Categories: evolutionary biology - Software type(s): website - tool
A modified BLAST, designed to query ortholog group data. It treats each ortholog group as a unit, and instead of providing a ranked list of individual sequence hits, it organizes and ranks the results by ortholog groups, which is often a much more desirable format for functional inference or evolutionary studies.
Categories: genomics, (similarity search), evolutionary biology - Software type(s): CLI - tool
BUSCO (Benchmarking Universal Single-Copy Orthologs) provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.
Categories: evolutionary biology - Software type(s): website - tool
This tool creates a dendrogram from (a) a set of variables or (b) from a similarity matrix. The program calculates a similarity matrix (only for option a), transforms similarity coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm.
Categories: evolutionary biology - Software type(s): website - tool
This program maps evolutionary traces to structures
Categories: genomics, (sequence alignment), evolutionary biology - Software type(s): CLI - tool
The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.
Categories: evolutionary biology - Software type(s): CLI - tool
PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables.
Categories: evolutionary biology - Software type(s): website, library - tool
Phylo.io is a state of the art tool for visualising and comparing phylogenetic trees on the web. It can be used to view a single tree, or compare the internal structure of two differently inferred trees for the same group of taxons. Phylo.io includes a number of useful features to make the viewing and comparing of even very large trees extremely easy.
Categories: evolutionary biology - Software type(s): website - tool
Compilation of links to 390 phylogeny packages and about 50 free web servers, arranged by several criteria.
Categories: evolutionary biology - Software type(s): website - tool
Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. It runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences.
Categories: evolutionary biology - Software type(s): website - tool
The PhylOgenetic Web Repeater (POWER) allows users performing phylogenetic analysis with molecular data by most programs of PHYLIP package repeatedly. POWER provide two pipelines to process the analysis. One of them includes multiple sequence alignment (MSA) at the begining of the pipeline whereas the other begin phylogenetic analysis with aligned sequence.