| -nt |
number (1 or more) |
Specify number of threads of execution (if built with OMP) |
| -no-banner |
|
Suppress banner |
| -v |
|
Verbose output |
| -bar |
|
Turns on the display of progress bars |
| -q |
|
Silent |
| -in |
dist input file path |
Supply path of a distance matrix file. |
| -fasta |
fasta input file path |
Supply path of a fasta format file containing an alignment |
| -phylip |
phylip input file path |
supply path of a phylip alignment file |
| -uncorrected |
|
with -fasta, do not apply Jukes-Cantor distance correction to calculated distances |
| -max-dist |
number |
specify the maximum distance that is to be allowed, when generating a distance matrix file (the default maximum is 10) |
| -not-dna |
|
with -fasta, indicates input is (not) DNA |
| -alphabet |
list of characters |
with -fasta, recognized nucleotide characters |
| -unknown |
list of characters |
with -fasta, characters that indicate unknown |
| -strip-name |
list of characters |
Characters to strip from taxon names (case sensitive) |
| -name-replace |
list of characters |
Characters to replace the stripped characters with |
| -truncate-name-at |
list of characters |
Truncate taxon name on one of these characters |
| -num |
|
Replace all taxon names with numbered names of the form A_i_ (i is taxon number, starting at 1) |
| -filter |
|
with -fasta, Filter sequences that have zero distances |
| -no-matrix |
|
with -fasta, save memory by not constructing the input matrix in memory (only has an effect with -t NONE) |
| -msa-out |
msa output file path |
given -fasta or -phylip, rewrite alignment in msa format |
| -dist |
dist output file path |
Supply path to which to write a distance matrix (makes sense with -in, -fasta or -phylip). Use STDOUT to write to standard output. |
| -dist-out |
distance matrix output file path |
Synonym for -dist. |
| -t |
algorithm name |
Specify the algorithm to use to construct the tree (or none) |
| -out |
newick output file path |
Use STDOUT to write it to standard output |
| -std-out |
|
Equivalent to -out STDOUT |
| -no-out |
|
Do not generate a newick output file |
| -gz |
|
Write outputs in gzip format |
| -out-format |
square, upper, lower |
format for writing distance matrix output |
| -f |
number 1-15 |
Digits of precision, to write in the output |
| -c |
number 0-9 |
Compression level to use when writing gzip files |