Results for "Phylogeny"

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  • iTOL: interactive Tree Of Life

    Interactive Tree Of Life is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize mid-sized tree (up to several thousand leaves). Trees...

    Tags: Bioinformatics, Tree, Phylogeny, Visualization, iTOL

    2614 days ago

  • Lifemap

    Lifemap is an interactive tool to explore the WHOLE NCBI TAXONOMY. The concept used in Lifemap is similar to the one used in cartography with tools like Google Maps© or Open Street Maps: exploring is done by zooming and panning.  The current tree contains ALL species present in NCBI ...

    Tags: Bioinformatics, Lifemap, Tree, Phylogeny, Taxonomy, Draw, View, Zoom, See, France, Interactive

    2545 days ago

  • Tetra-Nucleotide Analysis

    A tetra-nucleotide is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Pride et al. (2003) showed that the frequency of tetra-nucleotides in bacterial genomes contain useful, albeit weak, phylogenetic signals. Even though tetra-nucleotide analysis (TNA) utilizes the informat...

    Tags: Bioinformatics, Tetra-Nucleotide, Analysis, Frequency, DNA, Phylogeny, Algorithms

    2521 days ago

  • UPGMA Worked Example

    The tabs below include a walkthrough of clustering 7 biological sequences (A-G) using the Unweighted Pair-Group Method with Arithmetic mean (UPGMA) method. Note that UPGMA is actually a generic method and thus the walkthrough could apply to any objects A-G for which pairwise distances can be calc...

    Tags: UPGMA, Worked, Example, Tree, Phylogeny

    898 days ago

  • FigTree

    FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display su...

    Tags: figtree, tree, phylogeny, draw

    2445 days ago

  • Snippy: Rapid haploid variant calling and core SNP phylogeny

    Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a cons...

    Tags: Snippy, Rapid, haploid, variant, calling, core, SNP, phylogeny, bacteria

    1988 days ago

  • LibsDyogen: Libibrary for comparative genomics

    Library of usual classes and functions written in python and used in the Dyogen team for comparative genomics applications. Collaborative python library used in the DYOGEN teamfor studying the evolution of gene order in vertebrates. http://www.ibens.ens.fr/?rubrique43&lang=fr  

    Tags: LibsDyogen, Libibrary, comparative, genomics, phylogeny

    1556 days ago

  • VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs

    VCF2PopTree is a client-side software written in Javascript and it runs purely within the user’s computer/browser.  VCF2PopTree is compatible with all population browsers including Chrome, Opera, Edge and Firefox and works equally efficient in Mac, Windows and Linux (Ubuntu).  Fu...

    Tags: VCF2PopTree, client-side, software, construct, population, phylogeny, genome-wide, SNPs

    825 days ago

  • GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes

    A phylogeny based comparative genomics software to analyze the genetic environment of genes. The user can select one or several taxa and provide one or several reference protein(s). Genomes and plasmids (based on user choice) will be downloaded from the NCBI Assembly/NR database and searched for ...

    Tags: GEnView, phylogeny, comparative, genomics, software, analyze, genetic, environment, genes

    822 days ago