PVT
:: DESCRIPTION
PVT (Phylogenetic Visualization tool) using treemaps & taxonomic information.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
- Windows / Linux / MacOS
- Java
:: DOWNLOAD
:: MORE INFORMATION
Tag: Tool
trimAl 1.4 – Tool for Automated Alignment Trimming
trimAl 1.4
:: DESCRIPTION
trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Mac OsX / Linux / Windows
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon.
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Bioinformatics 2009 25: 1972-1973.
AbundanceBin 1.0.1 – Abundance-based tool for Binning Metagenomic Sequences
AbundanceBin 1.0.1
:: DESCRIPTION
AbundanceBin is an abundance-based tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes—-two important characteristic parameters for a microbial community.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Yu-Wei Wu and Yuzhen Ye.
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.
Lecture Notes in Computer Science2010, Volume 6044/2010, 535-549 (RECOMB 2010)
STRIKE 1.2 – Sequence Alignment Scoring Tool
STRIKE 1.2
:: DESCRIPTION
STRIKE (Single sTRucture Induced Evaluation) is a program to evaluate protein multiple sequence alignments using a single protein structure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2011 Dec 15;27(24):3385-91. doi: 10.1093/bioinformatics/btr587. Epub 2011 Oct 28.
STRIKE: evaluation of protein MSAs using a single 3D structure.
Kemena C, Taly JF, Kleinjung J, Notredame C.
Trebol 20111212 – Interactive Comparative Genomics Tool
Trebol 20111212
:: DESCRIPTION
Trebol is a multi-platform software for comparative genome analyses with functionalities such as sequence retrieving, generation of sequence comparisons, visualization, edition and rendering of high quality images for scientific publications.
::DEVELOPER
Millenium Institute of Oceanography
:: SCREENSHOTS
:: REQUIREMENTS
- Windows / MacOsX
:: DOWNLOAD
:: MORE INFORMATION
SHOT 2.0 – Shared Ortholog and Gene Order Tree Reconstruction Tool
SHOT 2.0
:: DESCRIPTION
SHOT is a web server for the classification of genomes on the basis of shared gene content or the conservation of gene order that reflects the dominant, phylogenetic signal in these genomic properties. In general, the genome trees are consistent with classical gene-based phylogenies, although some interesting exceptions indicate massive horizontal gene transfer. SHOT is a useful tool for analysing the tree of life from a genomic point of view
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Web Browser
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
SHOT: a web server for the construction of genome phylogenies.
Korbel JO, Snel B, Huynen MA, Bork P
Trends Genet. 2002 Mar; 18(3): 158-62. PubMed: 11858840.
KEX 1.21 – A simple Knowledge EXtraction tool
SoftSearch 1.0 – Structural Variant (SV) Detection tool
SoftSearch 1.0
:: DESCRIPTION
SoftSearch is a sensitive structural variant detection (SV) detection tool for Illumina paired-end next-generation sequencing data. SoftSearch simultaneously utilizes soft-clipping and read-pair strategies for detecting SVs to increase sensitivity.
::DEVELOPER
Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
- Perl
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2013 Dec 16;8(12):e83356. doi: 10.1371/journal.pone.0083356. eCollection 2013.
SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.
Hart SN1, Sarangi V1, Moore R1, Baheti S1, Bhavsar JD1, Couch FJ2, Kocher JP
PhyloGena 1.04 – Automated Interactive Phylogenetic Annotation Tool
PhyloGena 1.04
:: 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
- Windows/ Linux / Mac OsX
- JAVA
:: 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.
AutoDock 4.2.6 / AutoDockTools 1.5.6 – Suite of Automated Docking Tools
AutoDock 4.2.6
:: DESCRIPTION
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
AutoDockTools (ADT) is graphical front-end for setting up and running AutoDock – an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
::DEVELOPER
Molecular Graphics Laboratory , The Scripps Research Institute
:: SCREENSHOTS
:: REQUIREMENTS
- Windows / MacOsX / Linux
:: DOWNLOAD
:: MORE INFORMATION
Citation
Morris,G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson, A. J. (2009)
Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity.
J.Comput.Chem. 2009 Dec;30(16):2785-91.