This group is dedicated to Comparative genomics ... Dramatic results have emerged from the rapidly developing field of comparative genomics. Comparison of the fruit fly genome with the human genome reveals that about sixty percent of genes are conserved (Adams et al. 2000). That is, the two organisms appear to share a core set of genes. Researchers have also found that two-thirds of human genes known to be involved in cancer have counterparts in the fruit fly.
github.com - Pilon is a software tool which can be used to:
Automatically improve draft assemblies
Find variation among strains, including large event detection
Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads...
Evolutionary Dynamics and Population Genetics
Natural selection and other evolutionary forces lead to particular patterns of evolutionary dynamics, and they leave characteristic signatures on the genetic variation within populations. We use a...
bioinformatics.oxfordjournals.org - This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient...
darkhorse.ucsd.edu - DarkHorse is a bioinformatic method for rapid, automated identification and ranking of phylogenetically atypical proteins on a genome-wide basis. It works by selecting potential ortholog matches from a reference database of amino acid...
cancer.sanger.ac.uk - The accurate description and annotation of structural variants can be complex. This is due to the different resolution that variants are reported from traditional cytogenetic coordinates down to the actual base pair positions....
sourceforge.net - AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET...
sourceforge.net - _A5-miseq_ is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running _A5-miseq_.
Point to note:
There are many situations where A5-miseq is not...
drive5.com - USEARCH >Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >Multiple sequence alignment. Faster and more accurate than CLUSTALW.
UPARSE >OTU clustering for 16S and other marker genes....