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Updated QuickStart EukPhylo (markdown)

Adri K. Grow 2025-02-03 11:50:36 -05:00
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QuickStart-EukPhylo.md

@ -130,14 +130,14 @@ Basic running for building MSAs and Trees:
For additional input parameter options, see table below or run: `python phylotol.py --help`
|Flag|Options|Help|
|:---|:-------|:---|
|`--start`|default = `raw`, choices = `raw`, `unaligned`, `aligned`, `trees`|Stage at which to start running PhyloToL|
|`--end`|default = `trees`, choices = `unaligned`, `aligned`, `trees`|Stage until which to run PhyloToL. Options are `unaligned` (which will run up to but not including guidance), `aligned` (which will run up to but not including RAxML), and `trees` which will run through RAxML')|
|`--gf_list`|default = None|Path to the file with the GFs of interest. Only required if starting from the raw dataset|
|`--taxon_list`|default = None| Path to the file with the taxa (10-digit codes) to include in the output|
|`--data`|default = None|Path to the input dataset. The format of this varies depending on your --start parameter. If you are running the contamination loop starting with trees, this folder must include both trees AND a fasta file for each tree (with identical file names other than the extension) that includes an amino-acid sequence for each tip of the tree (with the sequence names matching exactly the tip names)|
|`--output`|default = `../`|Directory where the output folder should be created. If not given, the folder will be created in the parent directory of the folder containing the scripts|
|Flag|Options|Help|Default|
|:---|:-------|:---|:---|
|`--start`|choices = `raw`, `unaligned`, `aligned`, `trees`|Stage at which to start running PhyloToL|default = `raw`|
|`--end`|choices = `unaligned`, `aligned`, `trees`|Stage until which to run PhyloToL. Options are `unaligned` (which will run up to but not including guidance), `aligned` (which will run up to but not including RAxML), and `trees` which will run through RAxML')|default = `trees`|
|`--gf_list`|Path to the file with the GFs of interest. Only required if starting from the raw dataset|default = None|
|`--taxon_list`|Path to the file with the taxa (10-digit codes) to include in the output|default = None|
|`--data`|Path to the input dataset. The format of this varies depending on your --start parameter. If you are running the contamination loop starting with trees, this folder must include both trees AND a fasta file for each tree (with identical file names other than the extension) that includes an amino-acid sequence for each tip of the tree (with the sequence names matching exactly the tip names)|default = None|
|`--output`|Directory where the output folder should be created. If not given, the folder will be created in the parent directory of the folder containing the scripts|default = `../`|
### Modularity of options