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-partition <input-partition-format> --output-partition <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 --skip-checking 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-partition charset --output-partition nexus

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

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

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

All options

Option	Description
-i, --input	Partition files, or alignments with an embedded partition. Allows wildcards
-p, --input-partition	Input partition format: charset, nexus, or raxml
-P, --output-partition	Output partition format: nexus (default), charset, or raxml
--codon	Write the partition as a codon model
--datatype	Data type: dna (default), aa, or ignore. Sets the RAxML datatype label
--skip-checking	Skip checking the partition positions
-f, --input-format	Format of an alignment with an embedded partition: auto (default), fasta, nexus, or phylip
-F, --output-format	Output sequence format: nexus (default), phylip, fasta, nexus-int, phylip-int, or fasta-int
-o, --output	Output directory. Default: Partition-Convert
--force	Overwrite an existing output directory
--log	Log file path. Default: segul.log