Alligator v. Chicken
Links to data are in the "Links and Downloads" section of the results. Links of interest:
- SynMap syntenic gene pairs: "Final syntenic gene-set output with GEvo links"
- Information on parsing the file: 
- Mapping of alligator contigs to chicken: "Syntenic Path Assembly mapping"
Note: There is the option to screen syntenic regions using syntenic depth, but this option is not compatible with the syntenic path assembly. Screening with a 1:1 syntenic depth will remove most of the older syntenic regions derived from the most recent shared tetraploidy event in these lineages (useful for identifying syntenic orthologous genes. However, you won't produce as pretty of a graphic as when you use the syntenic path assembly.
- Syntenic depth 1:1 : http://genomevolution.org/r/5ed6
SynFind is another program that identifies syntenic genes using a different algorithm and procedure than SynMap. One difference is the ability to identify syntenic regions where a given gene is missing. Using this on a genome like alligator, with many small contigs, produces some interesting results. Namely, SynFind will identify many alligator contigs that are syntenic to a given chicken genomic region.
- Master syntenic table between chicken and alligator: http://genomevolution.org/CoGe/SynFind.pl?fid=21867937;qdsgid=2731;dsgid=19527;ws=20;co=3;sf=1;algo=last;get_master=1
- Information on parsing this table: http://genomevolution.org/wiki/index.php/SynFind#Master_syntenic_pairs_table
- SynFind analysis: http://genomevolution.org/r/5eea
By not using alligator gene models and using chicken gene models, more alligator contigs should be assembled against chicken:
- more hits will be counted in alligator on an exon-by-exon basis instead of gene-by-gene (may capture smaller alligator contigs)
- Missing gene models in Alligator do not create false negatives
- Should capture exons at alligator contigs boundaries that were not annotated (and join alligator contigs broken in a gene.