:: DESCRIPTION
PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PhyloSift: phylogenetic analysis of genomes and metagenomes.
Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA.
PeerJ. 2014 Jan 9;2:e243. doi: 10.7717/peerj.243.
:: DESCRIPTION
SPECTRE provides several new implementations of pre-published algorithms to construct phylogenetic trees and networks (more precisely split networks), along with an interactive graphical interface for visualizing planar split networks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2018 Mar 15;34(6):1056-1057. doi: 10.1093/bioinformatics/btx740.
SPECTRE: a suite of phylogenetic tools for reticulate evolution.
Bastkowski S, Mapleson D, Spillner A, Wu T, Balvociute M, Moulton V.
:: DESCRIPTION
JPhyloIO is an open source Java library for reading and writing phylogenetic file formats. The main aim is to provide access to various formats using a single interface, while being independent of the concrete application data model, to achieve maximal flexibility.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2019 Jul 22;20(1):402. doi: 10.1186/s12859-019-2982-3.
JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface.
Stöver BC, Wiechers S, Müller KF.
:: DESCRIPTION
PhyDE (Phylogenetic Data Editor) is a system-independent editor for DNA and amino acid sequence alignments, designed to assist anybody interested in phylogenetic or other comparative analyses of sequence data.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PhyloGena is a software tool to facilitate phylogenetic annotation of unknown sequences. It has a user-friendly graphical interface and you will intuitively learn how to use it. You can import 1, 10, 100, 1000? (see below) DNA or protein sequences and the program will search for similar sequences, construct a multiple alignment and subsequently a phylogenetic tree for all of them and show them to you. You can easily manipulate the data sets, add or remove sequences, change parameters etc. This is of great help in identifying the function and phylogenetic affiliation of ORFs and makes annotation of genes or ESTs easier and less error-prone.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hanekamp K, Bohnebeck U, Beszteri B, Valentin K.
PhyloGena–a user-friendly system for automated phylogenetic annotation of unknown sequences.
Bioinformatics. 2007 Apr 1;23(7):793-801. Epub 2007 Mar 1.
:: DESCRIPTION
DILTAG is an algorithm allowing to infer a set of optimal evolutionary histories for a gene cluster in a single species, according to a general cost model involving variable length duplications (in tandem or inverted), deletions, and inversions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
M. Lajoie, D. Bertrand and N. El-Mabrouk.
Inferring the Evolutionary History of Gene Clusters from Phylogenetic and Gene Order Data.
Mol Biol Evol. 2010 Apr;27(4):761-72. doi: 10.1093/molbev/msp271
:: DESCRIPTION
The PSODA project provides an open-source phylogenetic search tool that reads the same data file format as PAUP*
::DEVELOPER
Computational Science Laboratory
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
H. Carroll, M. Ebbert, M. Clement and Q. Snell,
PSODA: Better Tasting and Less Filling Than PAUP,
Proceedings of the 4th Biotechnology and Bioinformatics Symposium, October 2007, pp 74-78.
:: DESCRIPTION
MaxAlike algorithm aims at reconstructing a nucleotide sequence in a target species, based on a multiple sequence alignment and a phylogenetic tree of homologous sequences from other species. For each alignment position the probabilities of occurrence for each nucleotide are computed, considering the phylogenetic position of the target species in the tree.
::DEVELOPER
Center for non-coding RNA in Technology and Health (RTH)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
P. Menzel, P. F. Stadler and J. Gorodkin:
maxAlike: Maximum-likelihood based sequence reconstruction with application to improved primer design for unknown sequences,
Bioinformatics, 2011, 27, 317-325.
:: DESCRIPTION
PhyloSort is a Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units (OTUs).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Ahmed Moustafa and Debashish Bhattacharya
PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas
BMC Evolutionary Biology 2008, 8:6doi:10.1186/1471-2148-8-6
:: DESCRIPTION
ExAlt is a software program designed to predict alternatively spliced overlapping exons in genomic sequence. The program works in several ways depending on the available input. ExAlt can use information about existing gene structure as well as sequence conservation to improve the precision of its predictions. ExAlt can also make predictions when only a single genomic sequence is available.
::DEVELOPER
Jonathan E. Allen at the Center for Bioinformatics and Computational Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
The ExAlt software is OSI Certified Open Source Software.
Citation:
J. E. Allen and S. L. Salzberg. A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons.Algorithms for Molecular Biology, 1:14, 2006.