Showing 12 open source projects for "trees"

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  • 1
    com-hfg

    com-hfg

    java library for XML, HTML, or SVG generation + bioinformatics classes

    The com.hfg (hairyfatguy.com) library is a collection of utility classes that make it easy to construct XML, HTML, XHTML, or SVG in an object-oriented way from within your Java application or webapp. It also contains other IO utilities and bioinformatics classes for phylogenetic trees, taxonomy, and multi-chain proteins. Requires JDK1.8.
    Downloads: 0 This Week
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  • 2
    A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.
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  • 3
    TreeBASE is a database and web front end that stores phylogenetic trees and the data matrices used to generate them. The current iteration comprises a complete rewrite of the schema and web layer, and will include a web services layer.
    Downloads: 0 This Week
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  • 4
    Javamony

    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...
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  • 5
    IMPACT

    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
    Downloads: 1 This Week
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  • 6
    PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
    Downloads: 0 This Week
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  • 7
    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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  • 8
    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.
    Downloads: 0 This Week
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  • 9
    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
    Downloads: 0 This Week
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  • 10
    TreeSoft is a collection of softwares that build or manipulate phylogenetic trees.
    Downloads: 2 This Week
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  • 11
    IGRAFU is an open source program to integrate solutions to rebuild phylogenetic trees. It supports various well-known algorithms, such as Maximum Parsimony and Distance-matrix methods.
    Downloads: 0 This Week
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  • 12
    JPhylo is a Java based visualization program used to display sequences of phylogenetic trees.
    Downloads: 0 This Week
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