Ancient whole genome duplication (WGD) detection tools !
...d with 32 chromosomes (2n = 4x8 = 32) Download the tutorial for CDS and GFF annotation files mkdir -p...//www.life.illinois.edu/ming/downloads/Spontaneum_genome/Sspon.v20190103.gff3.gzgunzip *.gz First conda...1182 days ago
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BioRuby :Ruby packages for biologist
...igh descriptive power. Classes for Multiple alignment (Bio::Alignment), Gene Ontology(Bio::GO), PDB (Bio::PDB), FANTOM database(Bio::FANTOM), GFF (Bio::GFF) and KEGGOrthology (Bio::KEGG...3974 days ago
Awesome perl frameworks, libraries and software - PART 2
...t generator ikegami/perl-LWP-Protocol-AnyEvent-http - Event loop friendly HTTP and HTTPS backend for Perl's LWP ihh/gfftools - Perl scripts for working with the GFF format iamcal/perl-Flickr-AP...2521 days ago
Next generation sequencing in R or bioconductor environment
...entation rtracklayer rtracklayer provides an interface for exporting annotation feature data to various genome browsers and file formats (such as GFF). See the Small RNA Profiling...3651 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...nloaded tracks from dbSNP Also accepts: FASTA, GFF/GTF/GVF, BED, Wiggle, Cosmic,.../binding; Input: multiple: SGR/TXT, BED, BED6, GFF; if using prealigned sequence...digree data); updated April 2015 Input: FASTA, GFF3, GVF Output: CDR (condenser...2935 days ago
ArrayGen Next Generation Genome Browser Coming Soon !!!
...equencing data analysis. It is platform independent and much simpler to use. The main features are, it supports many standard file formats such as GFF, BED, GTF, FASTA, VCF, BAM an...3103 days ago
Download the gff files from NCBI using bash script/command
...Create a Directory mkdir genome_gff cd genome_gff # Look for genome assembly.../all/.+/)(GCF_.+)|\1\2/\2_genomic.gff.gz|' > genomic_file_fungi.../all/.+/)(GCA_.+)|\1\2/\2_genomic.gff.gz|' > genomic_file_bacteria.../all/.+/)(GCF_.+)|\1\2/\2_genomic.gff.gz|' > genomic_file_protozoa...2550 days ago
Plot custom gene density with R
library(karyoploteR) pp2276 days ago
Comment on "Sibelia: A comparative genomics tool"
...start > end. If you wish, you can obtain coordinates in GFF format. If you use the flag: -gff Then coordinates of synten...specifying flag: --allstages Files "blocks_coordsN.(txt|gff)" will contain their coordina...1312 days ago
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