YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-27 22:20:26 +08:00
Code Issues Packages Projects Releases Wiki Activity

Updated Utilities (markdown)

Katzlab 2024-08-09 17:53:17 -04:00
parent fd88db1f48
commit e141f9e601
1 changed files with 31 additions and 31 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

62
Utilities.md

@ -1,33 +1,33 @@
PhyloToL 6 includes a set of stand-alone utility scripts that aim to increase the power of the analysis done with or without the core PhyloToL pipeline. We divide these scripts into five main categories: basic statistics, composition tools, MSA tools, gene tree description, and contamination removal. PhyloToL 6 includes a set of stand-alone utility scripts that aim to increase the power of the analysis done with or without the core PhyloToL pipeline. We divide these scripts into five main categories: basic statistics, composition tools, MSA tools, gene tree description, and contamination removal
A summary of some of the scripts is divided by category here A summary of some of the scripts is divided by category here
| [Script name](https://github.com/Katzlab/PhyloToL-6/tree/main/Utilities) | Intent | Output | | Input | [Script name](https://github.com/Katzlab/PhyloToL-6/tree/main/Utilities) | Intent | Output |
| ------------------------------------------------------------------------ | ---------------------------------------------------------------------------------- | -------------------------------------------------------------------------- | | ----------------------------- | ------------------------------------------------------------------------ | ---------------------------------------------------------------------------------- | -------------------------------------------------------------------------- |
| Assess_transcriptomes_v2.0.py | Calculates the length, GC content, and coverage of assembled files | Spreadsheet containing the length, coverage, and GC of each transcript. | | Assembly and fasta tools | Assess_transcriptomes_v2.0.py | Calculates the length, GC content, and coverage of assembled files | Spreadsheet containing the length, coverage, and GC of each transcript. |
| Cluster_v2.0.py | Clusters sequences in a fasta file | Clustered fasta files | | | Cluster_v2.0.py | Clusters sequences in a fasta file | Clustered fasta files |
| GetTaxonomy_v1.0.py | Collects taxonomic classification of organisms from NCBI | Spreadsheet with NCBI taxonomy | | | GetTaxonomy_v1.0.py | Collects taxonomic classification of organisms from NCBI | Spreadsheet with NCBI taxonomy |
| GetUniqueTaxa_v1.0.py | Gets the unique taxa from a taxonomic classification | Spreadsheet with unique taxa | | | GetUniqueTaxa_v1.0.py | Gets the unique taxa from a taxonomic classification | Spreadsheet with unique taxa |
| Plot_transcriptomes_v2.0.py | Plots the length, coverage, and GC distribution of transcriptomes. | Plots of transcripts distribution. | | | Plot_transcriptomes_v2.0.py | Plots the length, coverage, and GC distribution of transcriptomes. | Plots of transcripts distribution. |
| QuerySRA_v1.0.py | Downloads assemblies from NCBI | Assemblies, IDs, and GCA or SRR codes. | | | QuerySRA_v1.0.py | Downloads assemblies from NCBI | Assemblies, IDs, and GCA or SRR codes. |
| ReadMapping_v2.0.py | Maps a group of trimmed reads to a reference | Sam/Bam files. | | | ReadMapping_v2.0.py | Maps a group of trimmed reads to a reference | Sam/Bam files. |
| SeqLenToCsv_v1.0.py | Calculates the length of DNA sequences in fasta files | Spreadsheet containing the length of all sequences. | | | SeqLenToCsv_v1.0.py | Calculates the length of DNA sequences in fasta files | Spreadsheet containing the length of all sequences. |
| SharedOGs_v1.0.py | Summarizes the gene family presence in fasta files | Spreadsheet with the gene families | | | SharedOGs_v1.0.py | Summarizes the gene family presence in fasta files | Spreadsheet with the gene families |
| | | | | | | | |
| | | | | Sequence composition analysis | CUB_v2.1.py | Summarizes the nucleotide composition of fasta files | Fasta file and several spreadsheets summarizing the nucelotide composition |
| CUB_v2.1.py | Summarizes the nucleotide composition of fasta files | Fasta file and several spreadsheets summarizing the nucelotide composition | | | GC_identifier_v1.0.py | Renames sequence ID by GC composition | Fasta files with relabeled sequence ID |
| GC_identifier_v1.0.py | Renames sequence ID by GC composition | Fasta files with relabeled sequence ID | | | PlotComps_v2.0.r | Produces GC3 width plots | GC3 width plots |
| PlotComps_v2.0.r | Produces GC3 width plots | GC3 width plots | | | Plotcomps_SppName_v1.0.R | Produces GC3 width plots with the species name and # seqs added to each plot | GC3 width plots |
| Plotcomps_SppName_v1.0.R | Produces GC3 width plots with the species name and # seqs added to each plot | GC3 width plots | | | | | |
| | | | | MSA tools | BacktranslateAlignment.py | Produces new nucleotide alignment from an amino acid alignment | Aligned nucelotide file |
| | | | | | CountTaxonOccurence_v2.0.py | Counts the occurences of each taxa in each gene family of a post guidance file | Spreadsheet with counts of taxa |
| BacktranslateAlignment.py | Produces new nucleotide alignment from an amino acid alignment | Aligned nucelotide file | | | friendlessness_v2.0.py | Describes the internal regions of insertion unique or nearly unique to a sequence | Spreadsheet with each sequence statistics |
| CountTaxonOccurence_v2.0.py | Counts the occurences of each taxa in each gene family of a post guidance file | Spreadsheet with counts of taxa | | | Gappiness_v2.0.py | Produces statistics on the terminal and internal gaps of an alignment | Spreadsheet with the paralogs statistics |
| friendlessness_v2.0.py | Describes the internal regions of insertion unique or nearly unique to a sequence | Spreadsheet with each sequence statistics | | | GuidanceWrapper_v2.1.py | Guidance wrapper that can be used in place of PhyloToL pipeline | Guidanced alignment files |
| Gappiness_v2.0.py | Produces statistics on the terminal and internal gaps of an alignment | Spreadsheet with the paralogs statistics | | | | | |
| GuidanceWrapper_v2.1.py | Guidance wrapper that can be used in place of PhyloToL pipeline | Guidanced alignment files | | Gene tree description | CladeSizes_v2.0.py | Describes clade sizes for different taxonomic groups | Spreadsheet describing clade sizes |
| | | | | | ColorByClade_v2.1.py | Visualizes placement of taxa by taxonomic group in trees | Colored trees |
| | | | | | ContaminationBySisters_v2.2.py | Summarizes the taxonomic distribution of sister sequences for each taxon in a tree | Two spreadsheets summarizing tree tips relationship |
| CladeSizes_v2.0.py | Describes clade sizes for different taxonomic groups | Spreadsheet describing clade sizes | | | RenameTips_v1.0.py | Renames the tip labels of trees to include metadata such as location and date | Renamed trees |
| ColorByClade_v2.1.py | Visualizes placement of taxa by taxonomic group in trees | Colored trees | | | | | |
| ContaminationBySisters_v2.2.py | Summarizes the taxonomic distribution of sister sequences for each taxon in a tree | Two spreadsheets summarizing tree tips relationship | | Stand-alone clade grabbing | CladeGrabbing_v2.1.py | Selects clades of interest from trees using taxonomic specifications | Phylogenetic trees |
| RenameTips_v1.0.py | Renames the tip labels of trees to include metadata such as location and date | Renamed trees |