CONSEL

Category(ies): Bioinformatics

Version: v0.1i

Author / Distributor:
Hidetoshi Shimodaira, Department of Mathematical and Computing Sciences Tokyo Institute of Technology, (The former institution is The Institute of Statistical Mathematics, Japan)

Description:

CONSEL calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection. CONSEL does not estimate the phylogenetic tree by itself, but CONSEL does read the output of the other phylogenetic packages, such as Molphy, PAML, PAUP*, and TREE-PUZZLE. CONSEL calculates the p-value using several testing procedures; the bootstrap probability, the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and the weighted Shimodaira-Hasegawa test. In addition to these conventional tests, CONSEL calculates the p-value based on the approximately unbiased test using the multi-scale bootstrap technique.

?CONSEL consists of small programs written in C language; seqmt, makermt, consel, catpv, catci, treeass, catass, makerep, catmt, catrep, randrep. The following

Please refer to CONSEL for more details.

altix: Not available on altix

pcluster: Not available on pcluster

rcluster,IOB: running program | Documentation | Installation | System

Running Program: also refer to submit jobs to queues at rcluster,IOB

Please refer to CONSEL for detail commands Example command:

/usr/local/consel/seqmt --molphy foo

bsub -q queueName /usr/local/seqmt --molphy foo -o filename.out

Documentation: Online document available at CONSEL website

Installation: source downloaded from CONSEL website.

System(s): Unix