JustinYoung's repositories
Papaver-Genomics
The genomic data for Papaver species
assembly_RNAseq_without_refgenome
this pipe composed by several perl scripts was mainly used to assembly RNA_seq
Augustus
Genome annotation with AUGUSTUS
awesome-bioinformatics-tools
A curated list of awesome Bioinformatics software, tools and resources
dfoil
DFOIL: Introgression Testing for Five Taxa
EVidenceModeler
source code for EVM
extract-seq-from-big_genome
extract dna seq from big-genomes based blast results with your query sequences
extract_longest_mRNA
since the annotated gene always possesses more than one copy of mRNA, and we need to use a sequence of CDS to represent its gene sequce, so we need to extract the longest mRNA or CDS to perform the following analysis. here the script is suitble for extracting the sequence
GenomeSyn
We developed GenomeSyn as a new tool for constructing and visualizing genome synteny, its novel design and implementation can serve as a necessary complement to the study of genomic synteny and structural variation and its visualization tools.
genomethreader
GenomeThreader gene prediction software.
libjson-rpc-cpp
C++ framework for json-rpc (json remote procedure call)
NGenomeSyn
Any Way to Show Multi genomic Synteny
orfipy
Fast and flexible ORF finder
PASApipeline
PASA software
perl1line.txt
collection of handy perl one-liner scripts
ProtParCon
An application framework for manipulating molecular data and identifying parallel and convergent amino acid replacements at the molecular level.
STAR
RNA-seq aligner
stringtie
Transcript assembly and quantification for RNA-Seq
trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly