PSMAlign – Progressive Stem Matching Alignment

PSMAlign

:: DESCRIPTION

PSMAlign is an open source tool that performs pairwise RNA secondary structures alignment based on the conserved stem pattern discovered. It enables alignment of large structures, such as those in the 23S ribosomal RNA family. Arbitrary pseudoknots are also allowed.

::DEVELOPER

Jimmy Ka Ho Chiu, Yi-Ping Phoebe Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
Perl

:: DOWNLOAD

PSMAlign

:: MORE INFORMATION

Citation

Pairwise RNA secondary structure alignment with conserved stem pattern.
Chiu JK, Chen YP.
Bioinformatics. 2015 Aug 13. pii: btv471.

STEM 2.0 / STEM-hy 1.0 – Species Tree Estimation using Maximum likelihood (with hybridization)

STEM 2.0 / STEM-hy 1.0

:: DESCRIPTION

STEM-hy is a program for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Java

:: DOWNLOAD

STEM / STEM-hy

:: MORE INFORMATION

Citation

Kubatko, L., B. C. Carstens, and L. L. Knowles. 2009.
STEM: Species Tree Estimation using Maximum likelihood for gene trees under coalescence,
Bioinformatics (2009) 25 (7): 971-973.doi: 10.1093/bioinformatics/btp079

STEM 1.3.8 – Short Time-series Expression Miner

STEM 1.3.8

:: DESCRIPTION

STEM is a Java program for clustering, comparing, and visualizing short time series gene expression data (eight time points or less). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database and supports GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category, identifying which temporal expression profiles were enriched for these genes.

::DEVELOPER

Systems Biology Group – Carnegie Mellon University

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOsX / Windows
Java

:: DOWNLOAD

STEM

:: MORE INFORMATION

Citation

J. Ernst, Z. Bar-Joseph.
STEM: a tool for the analysis of short time series gene expression data.
BMC Bioinformatics, 7:191, 2006.