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Download Perl scripts and other files referred to in the book

Bioinformatics resources : Databases

Bioinformatics resources : Software

Unix, Perl and R

Perl scripts from the book in Python version

Solutions to exercises

Typographical issues

Cambridge University Press

• EMBOSS

Pairwise alignment and database searches for sequence similiarity
• BLAST
• BLAST Command Line Applications User Manual
• BLAT
• FASTA

Multiple alignment
• ClustalW
• T-Coffee
• Muscle
• Jalview, Java-based multiple sequence alignment editor and viewer

Analysis of protein domains
• HMMER
• SMART

Identification and structural analysis of non-coding RNA
• Infernal ("INFERence of RNA ALignment")

Phylogeny
• PHYLIP (the PHYLogeny Inference Package)
• MrBayes

Prediction of transmembrane domains and signal peptides
• SignalP
• TMHMM

• Alignment of reads to a reference genome
  • BWA aligner
  • Bowtie
  • SOAP
  • Mosaik
• Assembly of reads to reconstruct a complete genome
  • SGA
  • ABySS
  • Meraculous
  • ALLPATHS-LG
• RNA-Seq tools; "Tuxedo" suite:
  • Bowtie
  • Tophat
  • Cufflinks
• Genome viewers
  • Integrative Genomics Viewer
  • Integrated Genome Browser
• Other NGS tools, including SNP calling
  • GATK The Genome Analysis Toolkit
  • SAMtools
  • SAM and BAM format specification
  • bedtools
  • IGV, Integrative Genomics Viewer
• SEQanswers - the next generation sequencing community

• Network Science website
• Bioinformatics Organization
• The journal "Briefings in bioinformatics"
• Many tools and algorithms relevant to next-generation sequencing applications have been published in Bioinformatics, and these are gathered together in a 'Bioinformatics for Next Generation Sequencing' virtual issue