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Updated PhyloToL Part 1: GF assignment (markdown)

Godwin Ani 2024-08-12 12:25:43 -04:00
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PhyloToL-Part-1:-GF-assignment.md

@ -71,11 +71,11 @@ Replacing the PhyloToL Hook DB with a user-defined set of gene families is strai
Role of each script
<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL1_Processing_Transcriptomes_scripts.png" width="100%">
Main inputs : A folder containing the assembled transcripts, a folder containing the Databases, and a folder containing the scripts.
*Optional inputs : Gcodes.txt and Conspecific.txt
Outputs : ReadyToGo files (AA and NTD), taxon summary, and sequence summary.
* The Gcodes.txt is a tab separated txt file containing the genetic code of the taxa. This will most likely not be needed except for some organisms like ciliates.
Example:
* Main inputs : A folder containing the assembled transcripts, a folder containing the Databases, and a folder containing the scripts.
* *Optional inputs : Gcodes.txt and Conspecific.txt
* Outputs : ReadyToGo files (AA and NTD), taxon summary, and sequence summary.
* *The Gcodes.txt is a tab separated txt file containing the genetic code of the taxa. This will most likely not be needed except for some organisms like ciliates.
* Example:
| Taxa | Genetic code |
| ----------- | --------- |