Software

iSEEM2

  • PhyEco: A phylogenetically informative marker gene database
    • Database package
    • Publication: D. Wu, G. Jospin, J.A. Eisen (2013). Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups, PLOS ONE 8(10): e77033. doi:10.1371/journal.pone.0077033
  • TreeOTU: Phylogenetic clustering of protein coding sequences into operational taxonomic units (OTUs)

iSEEM 1

  • Picante. Publicly available.
  • AMPHORA. Software for automated phylogenomic analysis for whole genome phylogenies and metagenomic analyses. Publicly available.
  • Amphora-2. Publicly available.
  • STAP. Software for automated alignment, phylogenetic analysis, and phylogeny based classification of rRNA sequences. Publicly available.
  • WATERs. Scientific workflow software for analysis of rRNA sequences. Publicly available.
  • PhylOTU. Software for phylogeny-based classification of rRNA OTUs. Publicly available.
  • MetaPASSAGE. Publicly available.
  • PhyloP. Publicly available.
  • Biotorrents. Website and software for bittorrent based sharing of biology related files. Publicly available.
  • Zorro. Software for automated masking of sequence alignments. Publicly available.

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