diff --git a/QuickStart-EukPhylo.md b/QuickStart-EukPhylo.md index ee4e5e1..96bd918 100644 --- a/QuickStart-EukPhylo.md +++ b/QuickStart-EukPhylo.md @@ -54,13 +54,13 @@ Here add detail of each option possible: * -2 = end script * --assembled_transcripts = Folder with Assembled transcripts in fasta format * -o = path to output folder -* --genetic_code = specified genetic code, name of .txt file with Genetic codes +* --genetic_code = specified genetic code, name of .txt file with Genetic codes; optional * -d = path to Databases folder * log.txt = if added to the end of the command, it will output a log file with progress, warning, or error messages ### Output: * ReadyToGo = AA, NTD -* Sequences summary +* Sequences statistics and summary ### Modularity of options and replacing the Hook database EukPhylo part 1 for transcriptomes is composed of 7 scripts. User can choose to start or stop at each step by changing the -1 and/or -2 options. @@ -87,13 +87,13 @@ Here add detail of each options possible: * -2 = end script * --cds = Folder with CDS files in fasta format * -o = path to output folder -* --genetic_code = specified genetic code, name of .txt file with Genetic codes +* --genetic_code = specified genetic code, name of .txt file with Genetic codes; optional * -d = path to Databases folder * log.txt = if added to the end of the command, it will output a log file with progress, warning, or error messages ### Output: * ReadyToGo = AA, NTD -* Sequences summary +* Sequences statistics and summary ### Modularity of options and replacing the Hook database EukPhylo part 1 for genomes is composed of 5 scripts. User can choose to start or stop at each step by changing the -1 and/or -2 options.