Siphy 0.5 – SIte-specific PHYlogenetic analysis

Siphy 0.5

:: DESCRIPTION

Siphy (SIte-specific PHYlogenetic analysis) analyzes multiple sequence alignments and single outs bases or small regions that are undergoing selection by looking at reduction in substitution rates and unexpected detecting substitution patterns. A specific program to detect conserved transcription factor binding sites is also available.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX /Windows
Java

:: DOWNLOAD

Siphy

:: MORE INFORMATION

Citation

Manuel Garber et al.
Identifying novel constrained elements by exploiting biased substitution patterns,
Bioinformatics 2009 25(12):i54-i62.

iGPS 1.0.1 – Prediction of Site-specific Kinase-substrate Relations from Phosphoproteomic data

iGPS 1.0.1

:: DESCRIPTION

iGPS is a software package for the prediction of in vivo site-specific kinase-substrate relations (ssKSRs) mainly from the phosphoproteomic data.

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

WIndows / Linux / MacOsX
Java

:: DOWNLOAD

iGPS

:: MORE INFORMATION

Citation

Chunxia Song, Mingliang Ye, Xinning Jiang, Guanghui Han, Zhou Songyang, Yexiong Tan, Hongyang Wang, Jian Ren, Yu Xue & Hanfa Zou.
Systematic analysis of protein phosphorylation networks from phosphoproteomic data.
Mol Cell Proteomics. 2012 Jul 13

Selecton 2.4 – Identification of Site-Specific Positive Selection & Purifying Selection

Selecton 2.4

:: DESCRIPTION

The Selecton server enables detecting the selective forces at a single amino-acid site. The ratio of non-synonymous (amino-acid altering) to synonymous (silent) substitutions, known as the Ka/Ks ratio, is used to estimate both positive and purifying selection at each amino-acid site.

::DEVELOPER

Selecton Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows /MacOsX

:: DOWNLOAD

Selecton

:: MORE INFORMATION

Citation

Stern, A., Doron-Faigenboim, A., Erez, E., Martz, E., Bacharach, E., Pupko, T.
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.
Nucleic Acids Research. 35: W506-W511.

SISSI 1.0 – Simulating Sequence Evolution with Site-Specific Interactions

SISSI 1.0

:: DESCRIPTION

SISSI (Simulating Sequence Evolution with Site-Specific Interactions) is a software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices.

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows /MacOsX

:: DOWNLOAD

SISSI

:: MORE INFORMATION

Citation:

Tanja Gesell and Arndt von Haeseler:
In silico sequence evolution with site-specific interactions along phylogenetic trees, Phylogenetic Trees.
Bioinformatics, 22:716-722, 2006.