Table 1.
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 |
Italicized text following option flags should be specified by the user.