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Added doc for simplot
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‎README.md‎

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* distances: compute evolutionary distances for nucleotide alignment
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* entropy: compute entropy of alignment sites
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* pssm: compute position-specific scoring matrix
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* simplot: compute similarity plot data + image
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* concat: Concatenates several alignments by concatenating each sequences having the same name
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* consensus: Compute a basic majority consensus of an input alignment
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* dedup: Remove sequences that have the same sequence

‎docs/commands/compute.md‎

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- `-n 3` : By column frequency compared to uniform frequency: same as -n 1, but divides by uniform frequency of the nt/aa (1/4 for nt, 1/20 for aa)
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- `-n 4` : Normalization "Logo".
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Option `-c` allows to add pseudo counts before normalization, and option `-l` log2 transforms the values.
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4. `goalign compute simplot`: See the [dedicated page](simplot.md). Compute a similarity plot between a query sequence and other sequences, using a sliding window.
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#### Usage
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distance Compute distance matrix from an input alignment
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entropy Computes entropy of a given alignment
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pssm Computes and prints a Position specific scoring matrix
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[simplot](simplot.md)) Computes simplot data and image
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Flags:
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-h, --help help for compute

‎docs/commands/compute_simplot.md‎

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# Goalign: toolkit and api for alignment manipulation
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## Commands
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### compute simplot
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This command takes as input:
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1. A sequence alignment,
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2. A query sequences that we want to compare to others
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It then computes evolutionary distances between the query sequence and all other sequences,
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for each region defined by sliding windows of size and step parameterizable.
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Query sequence name is defined by the following parameter:
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```
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-r, --refseq string Reference sequence to compare all others (default "-")
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```
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Sliding windows are defined by the following parameters:
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```
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-w, --window-size int Window size (default 100)
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-s, --window-step int Window step (default 100)
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```
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By default, `goalign compute simplot` only outputs distance data in the stdout or output file, in a tabluted format, with the columns:
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1. start (window start)
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2. end (window end)
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3. comp (compared sequence name)
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4. dist (computed distance between the query and the compared sequence on the current window)
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But `goalign compute simplot` can also generate a figure, if the following parameters are given:
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```
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--image string simplot image image output file (default "none")
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--image-height int simplot image output heigh (default 4)
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--image-width int simplot image image output width (default 4)
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```
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The output image format will depend on the name of the file (its extension).
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The evolutionary model to compute distances is specified using the following paramter:
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```
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-m, --model string Model for distance computation (default "k2p")
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```
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The model can take the following values:
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- pdist : number of mutations divided by length
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- rawdist : raw distance (like pdist, without normalization by length)
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- jc : Juke-Cantor
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- k2p : Kimura 2 Parameters
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- f81 : Felsenstein 81
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- f84 : Felsenstein 84
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- tn93 : Tamura and Nei 1993
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Finally, `goalign compute simplot` can group compared sequences into defined groups (e.g. clades, lineages, etc.). In this case, for each window, the distance is computed between the query sequences and each group of compared sequences, as the average distance between the query sequence and all members of each group. Groups are defined using sequence names (the information must be encoded into the sequence name). To do so, the following parameters must be given:
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```
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--group If sequences must be grouped
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--sep string Separator for extracting group (if group is true) (default "_")
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--field int Field number for extracting group (if group is true)
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```
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#### Usage
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```
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Usage:
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goalign compute simplot [flags]
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Flags:
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--field int Field number for extracting group (if group is true)
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--group If sequences must be grouped
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--image string LTT plot image image output file (default "none")
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--image-height int LTT plot image output heigh (default 4)
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--image-width int LTT plot image image output width (default 4)
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-m, --model string Model for distance computation (default "k2p")
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-o, --output string Distance matrix output file (default "stdout")
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-r, --refseq string Reference sequence to compare all others (default "-")
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--sep string Separator for extracting group (if group is true) (default "_")
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-w, --window-size int Window size (default 100)
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-s, --window-step int Window step (default 100)
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Global Flags:
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-i, --align string Alignment input file (default "stdin")
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--alphabet string Alignment/Sequences alphabet: auto (default), aa, or nt (default "auto")
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--auto-detect Auto detects input format (overrides -p, -x and -u)
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-u, --clustal Alignment is in clustal? default fasta
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--ignore-identical int Ignore duplicated sequences that have the same name and potentially have same sequences,
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0 : Does not ignore anything, 1: Ignore sequences having the same name (keep the first
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one whatever their sequence), 2: Ignore sequences having the same name and the same
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sequence
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--input-strict Strict phylip input format (only used with -p)
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-x, --nexus Alignment is in nexus? default fasta
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--no-block Write Phylip sequences without space separated blocks (only used with -p)
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--one-line Write Phylip sequences on 1 line (only used with -p)
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--output-strict Strict phylip output format (only used with -p)
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-p, --phylip Alignment is in phylip? default fasta
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-k, --stockholm Alignment is in stockholm? default fasta
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```
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#### Examples
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* Generating simplot for sars-cov-2 data from [Samson et. al](https://doi.org/10.1093/bioinformatics/btac287)
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```
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wget https://raw.githubusercontent.com/Stephane-S/Simplot_PlusPlus/refs/heads/master/example_data/sars_cov_2_gene_s.fas
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cat > rename.txt << EOF
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BetaCoV/Wuhan/IVDC-HB-04/2020 BetaCoV/Wuhan/IVDC-HB-04/2020_SARS-CoV-2
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BetaCoV/Wuhan/WIV04/2019 BetaCoV/Wuhan/WIV04/2019_SARS-CoV-2
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BetaCoV/Wuhan-Hu-1/2019 BetaCoV/Wuhan-Hu-1/2019_SARS-CoV-2
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GX/P1E GX/P1E_Guangxi-Pangolin-CoV
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GX/P2V GX/P2V_Guangxi-Pangolin-CoV
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GX/P3B GX/P3B_Guangxi-Pangolin-CoV
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GX/P4L GX/P4L_Guangxi-Pangolin-CoV
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GX/P5E GX/P5E_Guangxi-Pangolin-CoV
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GX/P5L GX/P5L_Guangxi-Pangolin-CoV
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bat-SL-CoVZC45 bat-SL-CoVZC45_BatCoVZ
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bat-SL-CoVZXC21 bat-SL-CoVZXC21_BatCoVZ
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BtCoV/BM48-31/BGR/2008 BtCoV/BM48-31/BGR/2008_BatCoV-Kenya
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BtKY72 BtKY72_BatCoV-Kenya
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Rs3367 Rs3367_BatSLCoVBTRS
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BtCoV/273/2005 BatCoV/273/2005_BatSLCoVBTRS
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BtCoV/279/2005 BatCoV/279/2005_BatSLCoVBTRS
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HKU3-13 HKU3-13_BatSLCoVHKU
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HKU3-6 HKU3-6_BatSLCoVHKU
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Rf1 Rf1_BatSLCoVHKU
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GD/P1L GD/P1L_GuangdongPangolinCoV
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GD/P2S GD/P2S_GuangdongPangolinCoV
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PC4_13 PC4-13_SARSCoV
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Tor2 Tor2_SARSCoV
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BetaCoV/bat/Yunnan/RaTG13/2013 BetaCoV/bat/Yunnan/RaTG13/2013_BatCoVRatG13
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EOF
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```
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**Simplot with individual sequences**:
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```
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goalign compute simplot -i sars_cov_2_gene_s.fas \
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--refseq BetaCoV/Wuhan-Hu-1/2019 \
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-w 200 -s 20 --image simplot_sars_cov_2_gene_s.png --image-height 10 --image-width 30
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```
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![Simplot individual sequences](simplot_sars_cov_2_gene_s.png)
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**Simplot with groups**:
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```
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goalign compute simplot -i sars_cov_2_gene_s_rename.fas \
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--refseq BetaCoV/Wuhan-Hu-1/2019_SARS-CoV-2 \
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-w 200 -s 20 --image simplot_sars_cov_2_gene_s_group.png --image-height 10 --image-width 30 \
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--group --field 1 --sep '_'
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```
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![Simplot by groups](simplot_sars_cov_2_gene_s_group.png)

‎docs/commands/simplot_sars_cov_2_gene_s.png‎

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‎docs/commands/simplot_sars_cov_2_gene_s_group.png‎

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‎docs/index.md‎

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-- | distance | Computes distance matrix from inpu alignment
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-- | entropy | Computes entropy of sites of a given alignment
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-- | pssm | Computes and prints a Position specific scoring matrix
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-- | [simplot](commands/compute_simplot.md) | Computes similarity plot data + image
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[concat](commands/concat.md) ([api](api/concat.md)) | | Concatenates a set of alignment
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[consensus](commands/consensus.md) ([api](api/consensus.md))| | Computes a basic majority consensus sequence
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[extract](commands/extract.md) | | Extracts sub-sequences from an input alignment

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