Genome Informatics Laboratory at KRIBB

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====== Unclassified topics ======
===== trimAl =====

  * 논문 [[https://www.ncbi.nlm.nih.gov/pubmed/19505945|PubMed]] 
  * http://trimal.cgenomics.org/ 
  * http://trimal.cgenomics.org/getting_started_with_trimal_v1.2

[[https://www.biostars.org/p/90005/|[BioStars] Removing gapped columns from a multiple sequence alignment]]
  trimal -in test -out test_nogaps_trimal -nogaps

Uses a heuristic method to decide which is the best automated method to trim the input alignment.

   trimal -in <inputfile> -out <outputfile> -automated1

===== FASconCAT =====

FASconCAT [[https://www.ncbi.nlm.nih.gov/pubmed/20416383|PubMed]] https://www.zfmk.de/en/research/research-centres-and-groups/fasconcat

===== Phylommand - a command line software package for phylogenetics =====

[[https://f1000research.com/articles/5-2903/v1|논문]] [[https://github.com/mr-y/phylommand|GitHub]]

===== getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories =====

[[https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04809-5|논문]] [[https://github.com/karubiotools/getSequenceInfo|GitHub]]

===== 기타 =====


[[https://academic.oup.com/nar/article/52/16/e74/7714450|GSearch: Ultra-Fast and Scalable Microbial Genome Search by combining Kmer Hashing with Hierarchical Navigable Small World Graphs]] [[http://enve-omics.ce.gatech.edu/data/gsearch|pre-built database]] [[https://github.com/jean-pierreBoth/gsearch|code]]