sngl_cp_gn The MIT License (MIT) Copyright (c) 2016 Alexander J Probst

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

CITATION: Probst et al., 2016 Environmental Microbiology "Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations", DOI: 10.1111/1462-2920.13362

This software was developed to estimate genome completeness of bacteria and archaea: scg.rb It requires a running version of usearch (64 bit).

Files designated with "DSTL_" are alternate version of scg.rb developed for "DAS Tool" and operate either with usearch (scg_blank.rb), diamond (scg_blank_diamond.rb) or with regular blast (scg_blank_blast.rb).

Provided databases for bacteria: bacteria_all.faa - contains full set of bacterial genomes bacteria_all.scg.faa - contains only single copy genes bacteria_all.scg.lookup - lookup table for single copy genes with annotations

Provided databases for archaea: archaea_all.faa - contains full set of bacterial genomes archaea_all.scg.faa - contains only single copy genes archaea_all.scg.lookup - lookup table for single copy genes with annotations