From 5e1aaba4a886b5e61c40cf0d916d65bae9cfdd9e Mon Sep 17 00:00:00 2001 From: Frederic Lemoine Date: Thu, 11 Oct 2018 10:41:19 +0200 Subject: [PATCH] Modified README and docs/index for new commands --- README.md | 3 +++ docs/index.md | 3 +++ 2 files changed, 6 insertions(+) diff --git a/README.md b/README.md index a39c106..3a86969 100644 --- a/README.md +++ b/README.md @@ -121,6 +121,7 @@ You may go to the [doc](docs/index.md) for a more detailed documentation of the * clean: Removes gap sites/sequences * sites : Removes sites with gaps * seqs : Removes sequences with gaps +* codonalign: Aligns a given nt fasta file using a corresponding aa alignment (by codons) * compute: Different computations (distances, etc.) * distances: compute evolutionary distances for nucleotide alignment * entropy: compute entropy of alignment sites @@ -130,6 +131,7 @@ You may go to the [doc](docs/index.md) for a more detailed documentation of the * divide: Divide an input alignment in several output files (one per alignment) * draw: Draw alignments * biojs: Display an input alignment in an html file using [BioJS](http://msa.biojs.net/) +* identical: Tells wether two alignments are identical * mutate: Adds substitutions (~sequencing errors), or gaps, uniformly in an input alignment * gaps: Adds gaps uniformly in an input alignment * snvs: Adds substitutions uniformly in an input alignment @@ -154,6 +156,7 @@ You may go to the [doc](docs/index.md) for a more detailed documentation of the * swap: Swap portions of some sequences (cut/paste) * stats: Prints different characteristics of the alignment * alleles + * alphabet * char * length * nalign diff --git a/docs/index.md b/docs/index.md index 2c375ae..6e6956e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -58,6 +58,7 @@ Command | Subcommand | [clean](commands/clean.md) ([api](api/clean.md)) | | Removes gap sites/sequences -- | sites | Removes sequences with gaps -- | seqs | Removes sites with gaps +[codonalign](commands/codonalign.md) ([api](api/codonalign.md))| | Different computations (distances, entropy, etc.) [compute](commands/compute.md) ([api](api/compute.md)) | | Different computations (distances, entropy, etc.) -- | distance | Computes distance matrix from inpu alignment -- | entropy | Computes entropy of sites of a given alignment @@ -68,6 +69,7 @@ Command | Subcommand | [divide](commands/divide.md) ([api](api/divide.md)) | | Divide an input alignment in several output files [draw](commands/draw.md) ([api](api/draw.md)) | | Draws an input alignment -- | biojs | Displays an input alignment in an html file using biojs +[identical](commands/identical.md) ([api](api/identical.md))| | Tells wether two alignments are identical [mutate](commands/mutate.md) ([api](api/mutate.md)) | | Adds substitutions (~sequencing errors), or gaps, uniformly in an input alignment -- | gaps | Adds gaps uniformly in an input alignment -- | snvs | Adds substitutions uniformly in an input alignment @@ -93,6 +95,7 @@ Command | Subcommand | [sort](commands/sort.md) ([api](api/sort.md)) | | Sorts the alignment by sequence name [stats](commands/stats.md) ([api](api/stats.md)) | | Prints different characteristics of the alignment -- | alleles | Prints the average number of alleles per sites of the alignment +-- | alphabet | Prints the alphabet detected for the alignment -- | char | Prints frequence of different characters (aa/nt) of the alignment -- | length | Prints the length of sequences in the alignment -- | maxchar | Prints max occurence char for each alignment site