This is a continously updated note about newly published bioinformatic tools. More will be said after trying to use them. Any comments on any of the topics or tools are appreciated.
#GWAS:
Covariate-modulated local false discovery rate for genome-wide association studies
Method: SNPs from categories enriched for non-null associations have a lower fdr for a given value of a test statistic than SNPs in unenriched categories. Test dataset: Eight Crohn’s disease substudies as independent training and test datasets.
#Whole Genome Evolution Simulation:
http://code.google.com/p/sgwe-project/
#RAD:
http://mbe.oxfordjournals.org/content/31/5/1272.full.pdf+html
#Phylogeny ####Incongruence among phylogenetic trees: RAxML.
#RNA-seq: ####PRADA: pipeline for RNA sequencing data analysis
####GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology(Measure the similarity of GO terms in two samples)