BOL

HGT-Finder: (i) can be used for HGT detection in both prokaryotes and eukaryotes, (ii) can report a statistical P value for each gene to indicate how likely it is to be horizontally transferred, and (iii) is fully automated (requires...

GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can...

Assessing an effective undergraduate module #teaching applied #bioinformatics to biology students http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005872

get the fasta genes using gff3 and genome.fa sequence: ~/Tools/bedtools2/bin/bedtools getfasta -fi vaga.fa -bed Adineta_vaga.v2.gff3 -fo Adineta_vaga_genes.fa

move to ~/.sshcd ~/.sshchmod 400 ~/.ssh/id_rsayou can add the config file to easy access.

FILE SPACING------------ # Double space a fileperl -pe '$\="\n"'perl -pe 'BEGIN { $\="\n" }'perl -pe '$_ .= "\n"'perl -pe 's/$/\n/'perl -nE 'say' # Double space a file, except the blank linesperl -pe '$_ .= "\n" unless /^$/'perl -pe '$_ .= "\n" if...

Dot, an interactive dot plot viewer that allows genome scientists to visualize genome-genome alignments in order to evaluate new assemblies and perform exploratory comparative genomics.  Dot supports the output of MUMmer’s nucmer aligner...

Graph visualization with R http://www.bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.pdf #R #Graph #Gviz #Visualisation

https://www.mitomap.org/MITOMAP -A compendium of polymorphisms and mutations in human mitochondrial DNA #mtDNA #DBs

http://premc.org/conferences/pemed-personalized-precision-medicine/ #Conference #diagnostics #bioinformatics #drug discovery #therapies #NGS #Paris

https://github.com/vinta/awesome-python #Python #frameworks #libraries #software #resources

http://code.makery.ch/library/javafx-8-tutorial/ #Java #UI #Coding

https://github.com/lauris/awesome-scala #Scala #Frameworks

https://medium.com/hashdog-blog/top-10-ruby-frameworks-3cc1214caae7 #Ruby #Web #Framework

http://12devs.co.uk/articles/writing-a-web-application-with-ruby-on-rails/ #Ruby #Web #Develpment

http://bioruby.org/ - BioRuby comes with a comprehensive set of free development tools and libraries for bioinformatics and molecular biology #RubyOnRail #BioInfo

Back in the early days of the web, many people learned Perl because of a wonderful Perl library called CGI. It was simple enough to get started without knowing much about the language and powerful enough to keep you going, learning by doing was...

There are several ways you can convert fastq to fasta sequences. Some methods are listed below. Using SED sed can be used to selectively print the desired lines from a file, so if you print the first and 2rd line of every 4 lines, you get the...