A tool to SPLit, Align and ConcatenatE genes sequences for phylogenetic inference.\
Cite:
Oliveira, R. R., Vasconcelos, S., & Oliveira, G. (2022). SPLACE: A tool to automatically SPLit, Align, and ConcatenatE genes for phylogenomic inference of several organisms. Frontiers in Bioinformatics, 2.
https://doi.org/10.3389/fbinf.2022.1074802
SPLACE will:
1.Split the same genes from different organisms;
2.Align each gene group separately;
3.Concatenate the aligned genes originated from the same organism.
Usage:
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./splace.sh -l <Fasta files list>.txt -t <num_threads> -o <output_name> -g <genes_list> -s <separator>
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./splace.sh -l <Fasta_files_list>.txt -t <num_threads> -o <output_name> -g <genes_list>
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#-l <Fasta_files_list> = Text file with a list of all fasta files to be included in the result.
#-t <num_threads> = Number or threads to use in the alignment step. Default is 1.
#-o <output_name> = Name of the result file to be generated.
#-g <genes_list> = If specified, any organism that do not have such gene, will have "?" in the supermatrix. If no specified, analysis is carried out only with the shared genes.
#-s = The separator character used to distinguish the gene name and any other information in the organisms fasta files.
./splace.sh -l filesList.txt -t 24 -o Glomeridesmus -g genes_list.txt -s _
Example of a Fasta_files_list.txt:
bases_genes_ITV1046I2.fasta
bases_genes_ITV8918.fasta
Example of a genes_list.txt:
nad1
cox1
nad2
cox2
atp6
The gene names must be the same in the fasta file of the different organisms, being necessary the use of the "_" separator between the gene name and any other gene specification or none separator and specification at all.
Ex: File bases_genes_ITV1046I2.fasta:
>atp8_ITV1046I2 atp8 ATP synthase F0 subunit 8 7816:7956 forward
attccacaaatatctccaataaattgagaaataatattcttaacttctattttaattctt
ttaataatttcaattattattcatcaaaactcaaattttaaattatctaaaagaaaaaaa
attccttcaaaaatttattaa
>atp6_ITV1046I2 atp6 ATP synthase F0 subunit 6 7964:8638 forward
atgataacaaatttattctcaatttttgatccttcttctattaccccaatttcactaaat
tgattaagtataattttaattataatttttataaatttaactttctggttattcaagtca
aaaaatcaaattattattaataatctaaattctatcattattaaggaattaaaaacaaca
ttaaaaacaagaaactatcctaactttattttaattttactaactttatttattttaatt
ttaattaataatttaataggtttattcccctatattttcacaagtacaagccacataata
attactttatcattagctttacctctatgatttatatccattataatattaataacaata
aacacaataaattttttagctcatctagttcctcaaagaactccttcttacttaatatcc
tttatagttttaattgaatctattagaaatattattcgaccaataacattagcaattcga
ctaacggctaatataattgctggacatcttttaatcactcttttaagatcaataaatgaa
aaaataaatattttttcatcaattattattattttatcttcaacaactctcataatctta
gaattagctgtagcaattattcaagcctacgtatttataactctattatcactatattta
agagaaattaattaa
Ex: File bases_genes_ITV8918.fasta
>atp8
attccacaaatatccccaataaattgagaaataatatttttaacttctattttaattctt
ttaataacttcaattattatccatcaaaattctaattttcgattatctaaaaaacaaaaa
attccttcaaaaatttattaa
>atp6
atgataacaaatttattctcaatttttgatccttcttctattacctcaatctcattaaat
tgattaagtatacttttaattataatctttataaatttaactttttgattatttaaatca
aaaaatcaaattcttattaataacctaaattctattattaataaagaattaaaaacaaca
ttaaaaacaagaaactaccctaattttattttaattttattaactttattcactctaatt
ttaattaataacttgataggcttatttccctacatctttacaagtacaagtcacataata
attactttatcattagctttacccctatgacttatatctattataatattaataataata
aatacaataaattttctagctcatctagtccctcaaagaactccttcatacttaatatcc
tttatagttttaattgaatctattagaaatattattcgaccaataacattagcaattcga
ttaactgctaatataattgccggacatcttttaattacccttttaagatcaataaatgaa
aaaataaatattttctcatcaattattattattttatcctcaacaatccttataattcta
gaattagctgtagcaatcattcaagcctacgtatttataactctactatcattatattta
agagaaatcaattaa
Results will be saved at the created folder <output_name>_results. In the folder <output_name>_genes will be created fasta file for each gene and its alignment.
A - To generate the supermatrix of n organisms, SPLACE will need n fasta files, each one containing all the g genes from a particular organism;
B - First, SPLACE splits the genes from an organism, gathering the genes that have the same name from the n organisms into a single fasta file, therefore generating g new fasta files, each one containing the same gene from different organisms (Figure 1B);
C - Then, SPLACE aligns each one of the g fasta files using the MAFFT aligner (with default parameter –auto), generating g’ new aligned fasta files;
D - Finally, the genes in the g’ aligned fasta files that came from the same organism are concatenated into a single sequence, generating a single fasta file with the supermatrix containing n sequences, each representing one of the n organisms;
E - Phylogeny can then be reconstructed using the supermatrix fasta file and the method of choice by the user.