A critical step before phylogenetic analysis and molecular selection analysis is to detect recombination and either remove recombinant sequences or partition the alignment into different spans that a recombination-free. The problem is that there are so many different recombination detection programs available. These have been nicely review by Posada (2002) and some of the programs […]
Read MoreI thought it was time for me to compile all the short command that I use on a more or less regular basis to manipulate sequence files. Convert a multi-line fasta to a singleline fasta awk ‘!/^>/ { printf “%s”, $0; n = “\n” } /^>/ { print n $0; n = “” } END […]
Read MoreUSE THE FOLLOWING RESPONSIBLY PLEASE! Recently, we wanted to send out a survey for the International Committee on Taxonomy of Viruses (ICTV) to a large number of authors who have recently published in a virology journal. Fortunately, PubMed stores author affiliations and the email address is also sometimes present in the affiliation. We decided to […]
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