AdaptML 1.0 – Partitioning of Gene Sequences according to their Genetic and Ecological Similarity

AdaptML 1.0

:: DESCRIPTION

AdaptML is a software package that will automatically partition groups of gene sequences according to both their genetic and ecological similarity.

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
Python

:: DOWNLOAD

AdaptML

:: MORE INFORMATION

Citation

Science. 2008 May 23;320(5879):1081-5. doi: 10.1126/science.1157890.
Resource partitioning and sympatric differentiation among closely related bacterioplankton.
Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF.

UIcluster 3.0.5 – Parallel Clustering of EST (Gene) Sequences

UIcluster 3.0.5

:: DESCRIPTION

UIcluster is an updated version of tlcluster that is much faster and adds new features such as reverse complement checking. In addition to optimization and reverse checking, it performs an extended search of all primaries for each sequence being clustered.

::DEVELOPER

Coordinated Laboratory for Computational Genomics (CLCG)

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Winodows / MacOsX
C Comipiler
Java

:: DOWNLOAD

UIcluster

:: MORE INFORMATION

Citation

K.T. Pedretti,
Accurate, Parallel Clustering of EST (Gene) Sequences,
Masters Thesis, Department of Electrical and Computer Engineering, University of Iowa, May 2001.

genBlastA 1.0.4 / genBlastG 1.39 – Homologous Gene Sequences

genBlastA 1.0.4 / genBlastG 1.39

:: DESCRIPTION

genBlast is a program suite, consisting of two programs: genBlastA and genBlastG.

genBlastA parses local alignments, or high-scoring segment pairs (HSPs) produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs. Each HSP group represent a putative gene that is homologous to the query protein (gene).

genBlastG is a fast homology-based gene finder. It builds on genBlastA. In particular, it takes genBlastA output as input and define gene models baesd on the HSP group.

::DEVELOPER

Jack Chen lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

genBlastA / genBlastG

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 1;27(15):2141-3. doi: 10.1093/bioinformatics/btr342. Epub 2011 Jun 8.
genBlastG: using BLAST searches to build homologous gene models.
She R1, Chu JS, Uyar B, Wang J, Wang K, Chen N.

Genome Res. 2009 Jan;19(1):143-9. doi: 10.1101/gr.082081.108. Epub 2008 Oct 6.
GenBlastA: enabling BLAST to identify homologous gene sequences.
She R1, Chu JS, Wang K, Pei J, Chen N.

SANTA-SIM 1.0 – Simulate the Evolution of Population of Gene Sequences Forwards through Time

SANTA-SIM 1.0

:: DESCRIPTION

SANTA-SIM is a forward-time simulator for gene sequences modeling a variety of mutation and selection processes.

::DEVELOPER

SANTA-SIM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS
Java

:: DOWNLOAD

SANTA-SIM

:: MORE INFORMATION

Citation:

SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination.
Jariani A, Warth C, Deforche K, Libin P, Drummond AJ, Rambaut A, Matsen Iv FA, Theys K.
Virus Evol. 2019 Mar 8;5(1):vez003. doi: 10.1093/ve/vez003.