Search Results for "phylogenetic"
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23 projects for "phylogenetic" with 1 filter applied:
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A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.
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Maximum Common Genome Alignment (MCGA)
Pipeline for creating core genome alignments for phylogenetic analysis
Maximum Common Genome Alignment (MCGA) Tool MCGA is a bioinformatics analysis tool written in Python for generating core genome alignment for bacterial whole genome sequences which can be used to construct phylogenetic trees. -
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Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.
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codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, codonPhyML will return the phylogenetic tree that best describes their evolutionary relationship. Our paper describing codonPhyML has been published in the journal "Molecular Biology and Evolution" (MBE). For more details, follow the link: http://mbe.oxfordjournals.org/content/30/6/1270. codonPhyML is on the cover of MBE! Check this out (August 2013): http://mbe.oxfordjournals.org/content/30/8.toc. ...
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DNATweezer
A suite of BioPerl wrappers for manipulating DNA and protein sequences
...These scripts provide command-line access to the most frequently used BioPerl DNA object methods e.g. reverse-complement and translation of DNA sequences, slicing a sequence alignment, rerooting a phylogenetic tree, and calculating diversity of a population of DNA sequences. -
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mx is a Ruby/Rails code base with broad application in evolutionary biology, it includes general functionality for matrix handling, sequence management, ontology construction, specimen handling, taxonomic catalogs, taxonomic descriptions and more
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GenNon-h
Simulating non-homogeneous multiple sequence alignments
A number of software packages are available to generate DNA MSAs evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages). GenNon-H is the first package designed to generate multiple sequence alignments under the discrete-time Markov processes on phylogenetic trees, which samples directly from the transition matrices. ... -
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Multiple optima
Scripts used to detect multiple optima of likelihood on real data.
R scripts and sequence data used in the paper "Multiple local maxima for likelihoods of phylogenetic trees constructed from biological data." by McComish BJ, Schliep KP and Penny D (submitted to Systematic Biology). -
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The Nexus Class Library (NCL) is a C++ library for interpreting data files created according to the NEXUS file format used in phylogenetic systematics and molecular evolution.
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Javamony
A Student's Approach to the Phylogenetic Problem
Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem. Javamony is invoked as follows: java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ... Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve fundamental problems in phylogenetics. ... -
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Pysimony
A Pythonic Implementation of Parsimony Inference of Phylogeny
...As all parts of the program are the original work of a beginner programmer, this may represent one of the worst approaches to solving the phylogenetic problem. I have clearly avoided object-oriented programming. Nevertheless, I distribute this imagining it might someday be slightly educational or at least provide a laugh at the pathetic attempt it makes to reinvent the wheel -
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EvoPromoter is a JAVA application that detects promoter regions in aligned nucleotide sequences using phylogenetic hidden markov models.
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A new open-source tool that integrates pipeline automated identification and phylogenetic studies of microbial communities using genes sequences
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IMPACT
Integrated Multiprogram Platform for Analyses in ConTest
Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A (2011) IMPACT: Integrated Multiprogram Platform for Analyses in ConTest. Journal of Heredity, 102 (3): 366-369. doi: https://doi.org/10.1093/jhered/esr003 -
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This is a wxWidgets-based, cross-platform graphical frontend for the maximum-likelihood phylogenetic inference program RAxML created by Alexis Stamatakis (A. Stamatakis, Bioinformatics 22(21):2688-2690, 2006)
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PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
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A tool to construct the metabolic networks from KEGG, and compare the constructed metabolic networks. Phylogenetic trees can be constructed along the case.
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TreeViewJ is a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches, and add names to nodes. Collection dates can be mapped onto a timeline, and sorted.
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A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
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PhyloPattern is a Java/Prolog API, helpful to simulate human reading of phylogenetic trees. Bioinformatician can: annotate trees, apply complex patterns to a tree to search specific architectures or extract information, compare trees with dynamically gen
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PhyloCpp is (will be...) a C++ toolkit designed for the reading, writing and manipulation of phylogenetic trees with an emphasis on comparative methods, ancestral state reconstruction and characterization of the evolutionary process.
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A collection of novel phylogenetics algorithms that assists biologists, geneticists, and bioinformaticians in the analysis and interpretation of phylogenetic data.
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