====== Installation instructions for building the bioinformatics apps in Impilo ======

As its first goal, Impilo provides on a single server the largest number of bioinformatics applications while also providing the most pertinent documentation on their uses for teaching and academic purposes.

===== Pairwise alignments =====
  *[[dotter|Dotter]]
  *[[blast|BLAST]]
  *[[fasta|FASTA]]

===== Multiple alignments =====
  *[[clustalw|CLUSTALW]] :!: 10.04 A10 update
  *[[clustalx|CLUSTALX]] :!: 10.04 A10 update
  *[[fsa|FSA]]
  *[[kalign|KAlign]]
  *[[mafft|MAFFT]]
  *[[muscle3|MUSCLE 3]]
  *[[tcoffee|T-COFFEE]]
  *[[strap|STRAP]]
  *[[jalview|JalView]]

===== Phylogeny - Analysis =====
  *[[beast|BEAST]]
  *[[gblocks|Gblocks]]
  *[[mesquite|Mesquite]]
  *[[mrbayes|MrBayes]]
  *[[phylip|PHYLIP]]
  *[[phylobayes|PhyloBayes]]
  *[[phyml|PhyML]]
  *[[raxml|RAxML]]

===== Phylogeny - Tree viewers and editors =====
  *[[archeopteryx|Archeopteryx]]
  *[[figtree|FigTree]]
  *[[njplot|NJPlot]]
  *[[tracer|Tracer]]
  *[[treefinder|Treefinder]]
  *[[treeview|TreeViewX]]

===== Gene annotation tools =====
  *[[rnamotif|RNAMotif]]
  *[[trnascan|tRNAScan-SE]]

===== Nucleic acid structural analysis =====
  *[[erpin|Erpin]]
  *[[unafold|UNAFOLD]]

===== Transcriptomics =====
  *[[spotfinder|TM4 Spotfinder]]
  *[[midas|TM4 MIDAS]]
  *[[rmaexpress|RMAExpress]]
  *[[mev|TM4 MeV]]

===== Integrative biology =====
  *[[cytoscape|Cytoscape]]
  *[[pathvisio|Pathvisio]]

===== Molecular modelling =====
  * [[jchempaint|JChemPaint]] :!: 10.04 A10 update
  * [[jmol|Jmol]] :!: 10.04 A10 update
  * [[pymol|Pymol]] :!: 10.04 A10 update
  * [[sirius|Sirius]]

===== Scientific Imagery =====
  * [[imagej|ImageJ]] :!: 10.04 A10 update

===== Biostatistics and calculation =====
  *[[R|R]] :!: 10.04 A10 update
  *[[bioconductor|Bioconductor]] :!: 10.04 A10 update

===== General purpose applications =====
  *[[artemis|Artemis]] :!: 10.04 A10 update
  *[[EMBOSS|EMBOSS / EMBASSY / Jemboss]] :!: 10.04 A10 update
  *[[Readseq|Readseq]] :!: 10.04 A10 update

===== Primer design and management =====
  *[[primer3|Primer3]] :!: 10.04 A10 update
  *[[primer3plus|Primer3Plus]]

===== High throughput sequencing =====
  *[[ingap|InGAP]] :!: 10.04 A10 removed
  *[[mira|MIRA 3]] :!: 10.04 A10 update
  *[[samtools|SAMtools]] :!: 10.04 A10 update
  *[[staden|Staden package]] :!: 10.04 A10 addition