BOL

halSynteny program makes it possible to speed up the computations by over two times in comparison with SatsumaSynteny2, another popular tool. Such high efficiency was attained by implementing a mathematically effective algorithm using C++.

https://phys.org/news/2020-06-scientists-synteny-blocks-animals.html

https://github.com/ComparativeGenomicsToolkit/hal/tree/master/synteny

halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments https://pubmed.ncbi.nlm.nih.gov/32463100/

Genome synteny analysis is the comparison of the genomic structure and gene content of two or more related species. Here are some general steps to follow for conducting a genome synteny analysis:

Choose the species: Select the species that you want to compare based on their evolutionary relationship or biological interest.

Obtain the genome sequences: Download the genome sequences of the selected species from a public database, such as NCBI or Ensembl.

Gene annotation: Annotate the genes in each genome using gene prediction software or tools such as MAKER.

Identify orthologous genes: Identify the orthologous genes between the genomes using tools such as OrthoFinder or OrthoMCL. Orthologous genes are genes that are homologous and have a common ancestor, but have diverged due to speciation.

Determine the synteny: Determine the synteny between the genomes by comparing the location and order of the orthologous genes. Synteny can be visualized using tools such as Circos or SynMap.

Interpret the results: Interpret the results of the synteny analysis by identifying conserved genomic regions, identifying gene families that have been lost or gained in specific lineages, and inferring the evolutionary history of the compared species.

Validate the results: Validate the results of the synteny analysis by comparing them to other sources of genomic data, such as gene expression or functional analysis.

Overall, genome synteny analysis is a complex process that requires a thorough understanding of genome structure, gene content, and evolutionary relationships between species. The analysis can provide insights into the genomic evolution of species and can be used to predict the function of genes in related species.