Synolog is a software pipeline for assigning gene orthologs and detecting conserved synteny.
Ortholog AssignmentSynolog detects orthologs using a combination of reciprocal best hit (RBH) BLAST between species and the detection of conserved syntney, ordered using a phylogenetic tree. This algorithm continues in rounds, detecting potential orthologs with BLAST and then combining the BLAST hits and conserved syntney locations to choose orthologs. Identifying Conserved SyntenySynolog identifies conserved synteny between genomes and provides extensive visualization tools to show genome-wide synteny, chromosome-specific synteny, or the synteny underliying a specific orthogroup. Genome Assembly CurationSynolog can be used to visualize and curate genome assemblies, using conserved gene synteny. Given a newly assembled genome, it can be compared visually, using orthologs, against other assemblies and changes can then be made to the assembly, which can then be reloaded into Synolog and re-visualized. |
Getting started with SynologFrequently Asked QuestionsTutorials |
Core |
Species Cache |
Execution control |
Utility programs |
Synolog is implemented in C++, with helper programs in Python, and is parallelized using the OpenMP libraries. It will compile on GNU-based Linux systems or BSD-based Apple OS X systems. Synolog is released under the GNU GPL license.
Synolog was developed by Gio Madrigal <> and Julian Catchen <>.
