Software
DiagHunterThe DiagHunter Perl script identifies diagonal features in a genomic dot plot, and displays these in dot plot images (.png files). These diagonals represent syntenic regions between two genomes, or internal duplications within one genome. DiagHunter also produces other text files that can be used for other types of analysis. The dot plots above (the small dense image and the sparse one with green lines) are two of the outputs from the program. These come from a comparison of the Arabidopsis thaliana chromosomes 4 and 2. See examples here of comparisons between all Arabidopsis chromosomes (as well as some mouse x human comparisons). If you are interested in this problem or data, please also check Alexander Kozik's program genoPix2D. genoPix2D is an interactive viewer of this kind of data, and can plot the output from DiagHunter (DiagHunter is also included in the genoPix2D distribution). This is beta software. So that I can send occasional notices of software updates, please provide an email address here. You may also email me with comments or questions at cann0010'at'tc.umn.edu.
README_DiagHunter OrthoParaMapOrthoParaMap combines comparative genomic positional information and phylogenetic reconstructions to identify which gene duplications are likely to have arisen through internal genomic duplications (such as polyploidy), through speciation, or through local duplications (such as unequal crossing-over). Read the abstract of a submitted manuscript on OrthoParaMap here: Abstract of "Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies" This is beta software. So that I can send occasional notices of software updates, please provide an email address here. You may also email me with comments or questions at cann0010'at'tc.umn.edu.
OPM_README GeneFamilyPipeThese are the scripts that I use in my day-to-day research. I make this available as-is, with no guarantees that it will work for you. Primarily, these scripts control lots of other bioinformatics programs, and manage format conversions and some data clean-up associated with phylogenetic tree construction. The nature of the process is that it requires the installation of a lot of other software. Much of this is standard stuff in bioinformatics, but it does require quite a bit of work to install. I have made some installation instructions here. Beyond these instructions, I have to say you're on your own in doing the installations.
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