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. 2024 Sep 24;12(6):e11604. doi: 10.1002/aps3.11604

Table 1.

Command‐line flags for BAD2matrix.

Option flag a Description Required
‐a 2 | 3 | 4 | 5 | 6|6dso|6kgb|6sr | 8 | 10 | 11 | 12 | 15 | 18 | 20 Number of amino acid states (default = 20). Reduction with option “6dso” follows Dayhoff et al. (1978); option “6kgb” follows Kosiol et al. (2004); option “6sr” follows Susko and Roger (2007); option “11” follows Buchfink et al. (2015); and all other options follow Murphy et al. (2000). No
‐d directory‐name Specify the input directory of aligned FASTA files. Names should use the following convention: “>species#sequenceID”. Characters other than letters, numbers, periods, and underscores will be deleted. Use “‐f” for an alternate naming convention. Yes
‐f Use full FASTA names rather than default settings (see “‐d” description for default). Characters other than letters, numbers, periods, and underscores will be deleted. No
‐g Do not code gene content (absence/presence). If this flag is not set, gene content is coded. No
‐i Do not code indels. If this flag is not set, indels are coded. No
‐m x Retain the upper x percentile of genes in the distribution of missing sequences. By default, x = 1 (i.e., include all genes with four or more sequences). No
‐n root‐name Specify the root‐name for output files. Yes
‐r Folder containing a morphological matrix or a set of ortholog duplication matrices. Datasets should be saved as .tsv tables. Multiple states should be separated by pipes ("|"). No
a

Italicized text following option flags should be specified by the user.