Table 2.
Command line parameters
| Program (version) | Parameters | Description |
|---|---|---|
| ProGraphMSA | -i 2 –mldist | Iterate distance and guide tree estimation two times |
| –no_force_align –end_indel_prob -1 | No special treatment of terminal gaps | |
| –fasta -o prograph.fasta input.fasta | Input/output | |
| ProGraphMSA+TR | –repeats –custom_tr_cmd trust2treks.py | Use TRUST for TR detection |
| –repeat_indel_rate 0.1 | TR unit insertion/deletion rate (per site) | |
| –repeat_indel_ext 0.3 | TR units insertion/deletion length coefficient | |
| -i 2 –mldist | Iterate distance and guide tree estimation two times | |
| –no_force_align –end_indel_prob -1 | No special treatment of terminal gaps | |
| –fasta -o prographTR.fasta input.fasta | Input/output | |
| ProGraphMSA+realTR | –read_repeats repeats.treks | Use true repeat information |
| –repeat_indel_rate 0.1 | TR unit insertion/deletion rate (per site) | |
| –repeat_indel_ext 0.3 | TR units insertion/deletion length coefficient | |
| -i 2 –mldist | Iterate distance and guide tree estimation two times | |
| –no_force_align –end_indel_prob -1 | No special treatment of terminal gaps | |
| –fasta -o prographRealTR.fasta input.fasta | Input/output | |
| MAFFT 6.843-with-ext | –maxiterate 1000 –globalpair | Iterative refinement (suggested for best results) |
| –quiet input.fasta > mafft.fasta | Input/output | |
| MUSCLE 3.8.31 | -quiet -in input.fasta -out muscle.fasta | Input/output |
All versions of ProGraphMSA have common parameters to iterate the estimation of distances and guide tree and to disable the special treatment of terminal gaps, which are enabled by default to deal with real sequence data. Further, the TR versions use the same TR unit indel distributions but use different sources for TR information. ProGraph+TR uses a TR-MSA produced by TRUST, whereas ProGraph+realTR uses the true TR unit information provided by the simulation algorithm. MUSCLE was executed with the default parameters and MAFFT with the parameters that were suggested in the command line help for best results.