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Alignment Partition Conversion

SEGUL CLI can convert single and multiple partition files. It can also extract partitions embedded in NEXUS sequence files.

segul partition convert --input <a-path/wildcard-to-partition> --input-part <input-partition-format> --output-part<output-partition-format>

If you output to RaXML partition and it is a DNA sequence, we recommend using the --datatype dna option. The partition format will include the datatype as below:

DNA, locus_1 = 1-100
DNA, locus_2 = 101-150
DNA, locus_3 = 151-200

By default, segul checks the partition format:

  1. The first partition position starts with 1.
  2. The next partition is the next number after the previous partition's end. If using the codon model, the next locus applies the rule.

Passing the --uncheck flag allows you to ignore format checking. For example, to extract nexus in-file partitions (called charset format in segul):

segul partition convert --input concatenated_alignment.nex --input-part charset --output-part nexus

You can also use wildcard to convert multiple concatenated alignment partitions at once:

segul partition convert --input ./*/concatenated_alignment.nex --input-part charset --output-part nexus

By default, SEGUL will save the resulting partitions in the parent directory of the input partition (or alignment if the partition is charset).