Sequence Quality Assessment Tool
SQUAT (sequence quality assessment tool) is a computerized stand-alone tool to assess quality of HIV protease (PR) and reverse transcriptase (RT) sequences prior to analyses. It was designed for Microsoft-Windows-running computers in an R statistical environment combined with Perl scripts. SQUAT steps include FASTA sequence file and related information submission; HIV PR and/or RT sequence identification; sequence alignment; screening for ambiguous nucleotides, frameshifts, insertions and deletions on the nucleic acid (NA) level; calculation of pairwise genetic distances and generation of a genetic distance histogram and a phylogenetic tree output; translation of NA into amino acids (AA); identification of ambiguous and atypical AA, stop codons and frameshifts on the AA level; and generation of a summary text file, aligned NA sequence output file, and two AA sequence output files of approved sequences, one with mixtures and one without mixtures.