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CLI Usages

📄️ Multi Alignment Format Conversion (Beta)

Multiple Alignment Format (MAF) is a text-based format for representing multiple sequence alignments. Unlike the NEXUS or PHYLIP format, which usually contains a single alignment, each MAF file can contain multiple alignments. This format helps store alignments with detailed information about the sequences, such as the sample name, scores, size, strand, and other attributes. However, most phylogenetic software does not support this format. SEGUL aims to bridge this gap by converting MAF files to FASTA or PHYLIP format, including support for interleaved and sequential formats. The output will be in multiple files containing sequences with a matching locus/gene. The filenames will be the locus/gene names.

📄️ Sequence Filtering

The sequence filtering method works at the sequence level, which differs from the SEGUL alignment filtering feature, which works on the alignment level. Using the alignment filtering feature will filter the entire alignment that does not meet the filtering criteria. However, the sequence filtering feature will remove sequences that do not meet the criteria while retaining the same alignment if at least one sequence is left in the alignment. The feature works on many alignments simultaneously and will never overwrite your original datasets; it will create new files with the filtered sequences.