https://github.com/applicativesystem/alignmentgo

a cloud native application for large scale phylogenomics
https://github.com/applicativesystem/alignmentgo

genome-alignment genome-alignment-utilites genome-analysis genome-annotation genomes-comparison phylogenomics phylogenomics-bioinformatics

Last synced: 7 days ago
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a cloud native application for large scale phylogenomics

• Host: GitHub
• URL: https://github.com/applicativesystem/alignmentgo
• Owner: applicativesystem
• License: mit
• Created: 2024-09-17T12:16:42.000Z (3 months ago)
• Default Branch: main
• Last Pushed: 2024-10-20T19:19:56.000Z (2 months ago)
• Last Synced: 2024-12-09T01:39:30.319Z (14 days ago)
• Topics: genome-alignment, genome-alignment-utilites, genome-analysis, genome-annotation, genomes-comparison, phylogenomics, phylogenomics-bioinformatics
• Language: Go
• Homepage:
• Size: 3 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# alignmentGO 

- a golang package for phylogenomics

- all the alignment utilites combined with a http server in a single genome scale package.

- This single application bring together all the functions i coded previously in a single package.

- All single package will be still available from my github repository and this complete package will be available from GO packages. \

  https://github.com/codecreatede/golang-reference-alignment-estimate \

  https://github.com/codecreatede/golang-alignment-block-genotyper-eDNA \

  https://github.com/codecreatede/goroutines-phylogenomics-filter \

  https://github.com/codecreatede/golang-alignment-block-getter \

  https://github.com/codecreatede/go-alignment-estimate \

  https://github.com/codecreatede/go-phylogenomics-tab \

  https://github.com/codecreatede/goroutines-alignment-merger \

  https://github.com/codecreatede/go-alignment-block-estimate \

  https://github.com/codecreatede/go-alignment-proportion 

- it deals with the complete phylogenomics and perfom all the work of the phylogenomics

- from alignment to the merging, filtering and generating the bootstrap phylogenomes.

```

➜  alignmentGO git:(main) ✗ go run main.go

This is a complete alignmentGo package for the phylogenomics and whole genome alignment

Usage:

  flags [command]

Available Commands:

  completion  Generate the autocompletion script for the specified shell

  estimate

  help        Help about any command

  merge

  unified

Flags:

  -h, --help   help for flags

Use "flags [command] --help" for more information about a command.

➜  alignmentGO git:(main) ✗ go run main.go estimate -h

This estimates the site by site alignment estimates across the alignment and it takes the first genome 

as a reference for the estimation of the site variablitiy

Usage:

  flags estimate [flags]

Flags:

  -h, --help           help for estimate

  -a, --title string   alignment file for the estimate (default "alignment file")

➜  alignmentGO git:(main) ✗ go run main.go merge -h

This merges all the alignment and gives the alignment ID header you have specified

Usage:

  flags merge [flags]

Flags:

  -A, --alignmentfile string   a alignment file (default "align")

  -h, --help                   help for merge

  -T, --title string           alignment title (default "title for the alignment")

➜  alignmentGO git:(main) ✗ go run main.go unified -h

This estimates the site proportion in your whole genome or gene specific alignment

Usage:

  flags unified [flags]

Flags:

  -a, --alignmentfile string   a alignment file (default "align")

  -h, --help                   help for unified

```

Gaurav Sablok