josephryan/exoblast
compare genome assemblies using sequence similarity to transcript or protein sequences from a different species.
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josephryan
Discovered public repositories for josephryan in the GitHub catalog.
josephryan/alien_index
identify potential non-animal transcripts in animal transcriptomes
josephryan/phyloconverge
an algorithm to look for convergent signals in phylogenetic trees
josephryan/JFR-PerlModules
Perl extensions for dealing with molecular sequence data formats (FASTA, FASTQ, GFF3, and more)
josephryan/sowhat
Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)
josephryan/estimate_genome_size.pl
Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
josephryan/isoblat
use RNA transcripts to assess assembly - this program parses the output of a BLAT run of transcriptome vs. a genome. It returns 1) Total % mapped, 2) average %coverage of a mapping, and 3) number of transcripts mapping to a single contig/scaffold. It is simple to run. Just run the blat (transcripts vs. genome) and then run the script with the blat-output and your transcript-fasta-file as arguments.