Goalign: toolkit and api for alignment manipulation
December 11, 2025 ยท View on GitHub
Commands
compute simplot
This command takes as input:
- A sequence alignment,
- A query sequences that we want to compare to others
It then computes evolutionary distances between the query sequence and all other sequences, for each region defined by sliding windows of size and step parameterizable.
Query sequence name is defined by the following parameter:
-r, --refseq string Reference sequence to compare all others (default "-")
Sliding windows are defined by the following parameters:
-w, --window-size int Window size (default 100)
-s, --window-step int Window step (default 100)
By default, goalign compute simplot only outputs distance data in the stdout or output file, in a tabluted format, with the columns:
- start (window start)
- end (window end)
- comp (compared sequence name)
- dist (computed distance between the query and the compared sequence on the current window)
But goalign compute simplot can also generate a figure, if the following parameters are given:
--image string simplot image image output file (default "none")
--image-height int simplot image output heigh (default 4)
--image-width int simplot image image output width (default 4)
The output image format will depend on the name of the file (its extension).
The evolutionary model to compute distances is specified using the following paramter:
-m, --model string Model for distance computation (default "k2p")
The model can take the following values:
- pdist : number of mutations divided by length
- rawdist : raw distance (like pdist, without normalization by length)
- jc : Juke-Cantor
- k2p : Kimura 2 Parameters
- f81 : Felsenstein 81
- f84 : Felsenstein 84
- tn93 : Tamura and Nei 1993
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:
--group If sequences must be grouped
--sep string Separator for extracting group (if group is true) (default "_")
--field int Field number for extracting group (if group is true)
Usage
Usage:
goalign compute simplot [flags]
Flags:
--field int Field number for extracting group (if group is true)
--group If sequences must be grouped
--image string LTT plot image image output file (default "none")
--image-height int LTT plot image output heigh (default 4)
--image-width int LTT plot image image output width (default 4)
-m, --model string Model for distance computation (default "k2p")
-o, --output string Distance matrix output file (default "stdout")
-r, --refseq string Reference sequence to compare all others (default "-")
--sep string Separator for extracting group (if group is true) (default "_")
-w, --window-size int Window size (default 100)
-s, --window-step int Window step (default 100)
Global Flags:
-i, --align string Alignment input file (default "stdin")
--alphabet string Alignment/Sequences alphabet: auto (default), aa, or nt (default "auto")
--auto-detect Auto detects input format (overrides -p, -x and -u)
-u, --clustal Alignment is in clustal? default fasta
--ignore-identical int Ignore duplicated sequences that have the same name and potentially have same sequences,
0 : Does not ignore anything, 1: Ignore sequences having the same name (keep the first
one whatever their sequence), 2: Ignore sequences having the same name and the same
sequence
--input-strict Strict phylip input format (only used with -p)
-x, --nexus Alignment is in nexus? default fasta
--no-block Write Phylip sequences without space separated blocks (only used with -p)
--one-line Write Phylip sequences on 1 line (only used with -p)
--output-strict Strict phylip output format (only used with -p)
-p, --phylip Alignment is in phylip? default fasta
-k, --stockholm Alignment is in stockholm? default fasta
Examples
- Generating simplot for sars-cov-2 data from Samson et. al
wget https://raw.githubusercontent.com/Stephane-S/Simplot_PlusPlus/refs/heads/master/example_data/sars_cov_2_gene_s.fas
cat > rename.txt << EOF
BetaCoV/Wuhan/IVDC-HB-04/2020 BetaCoV/Wuhan/IVDC-HB-04/2020_SARS-CoV-2
BetaCoV/Wuhan/WIV04/2019 BetaCoV/Wuhan/WIV04/2019_SARS-CoV-2
BetaCoV/Wuhan-Hu-1/2019 BetaCoV/Wuhan-Hu-1/2019_SARS-CoV-2
GX/P1E GX/P1E_Guangxi-Pangolin-CoV
GX/P2V GX/P2V_Guangxi-Pangolin-CoV
GX/P3B GX/P3B_Guangxi-Pangolin-CoV
GX/P4L GX/P4L_Guangxi-Pangolin-CoV
GX/P5E GX/P5E_Guangxi-Pangolin-CoV
GX/P5L GX/P5L_Guangxi-Pangolin-CoV
bat-SL-CoVZC45 bat-SL-CoVZC45_BatCoVZ
bat-SL-CoVZXC21 bat-SL-CoVZXC21_BatCoVZ
BtCoV/BM48-31/BGR/2008 BtCoV/BM48-31/BGR/2008_BatCoV-Kenya
BtKY72 BtKY72_BatCoV-Kenya
Rs3367 Rs3367_BatSLCoVBTRS
BtCoV/273/2005 BatCoV/273/2005_BatSLCoVBTRS
BtCoV/279/2005 BatCoV/279/2005_BatSLCoVBTRS
HKU3-13 HKU3-13_BatSLCoVHKU
HKU3-6 HKU3-6_BatSLCoVHKU
Rf1 Rf1_BatSLCoVHKU
GD/P1L GD/P1L_GuangdongPangolinCoV
GD/P2S GD/P2S_GuangdongPangolinCoV
PC4_13 PC4-13_SARSCoV
Tor2 Tor2_SARSCoV
BetaCoV/bat/Yunnan/RaTG13/2013 BetaCoV/bat/Yunnan/RaTG13/2013_BatCoVRatG13
EOF
Simplot with individual sequences:
goalign compute simplot -i sars_cov_2_gene_s.fas \
--refseq BetaCoV/Wuhan-Hu-1/2019 \
-w 200 -s 20 --image simplot_sars_cov_2_gene_s.png --image-height 10 --image-width 30
Simplot with groups:
goalign compute simplot -i sars_cov_2_gene_s_rename.fas \
--refseq BetaCoV/Wuhan-Hu-1/2019_SARS-CoV-2 \
-w 200 -s 20 --image simplot_sars_cov_2_gene_s_group.png --image-height 10 --image-width 30 \
--group --field 1 --sep '_'
