Software
GOLDVARB X (2005)
GOLDVARB X is a new version of the key methodological tool of variationist sociolinguistics – the variable rule program. This update of the program has been rewritten in C++ and runs in OS X. It is now compatible with either Macintosh or Windows environments and operates similarly in both. In addition, it has been revised to include a number of useful new user-interface features.
The manual for GoldVarb 2 is still a useful reference for GOLDVARB X, since the functions are essentially the same in the new version. Only the look is different. GoldVarb 2.x runs on Macintosh operating systems prior to OS X version 10.3.9.
PATHGROUPS
The PATHGROUPS program optimizes the gene order at ancestral nodes of a given phylogeny, given the order in modern genomes. (On the PATHGROUPS approach to rapid small phylogeny, C Zheng and D Sankoff, BMC Bioinformatics 2011)
Scaffold-filling
Scaffold-filling inserts genes from a fully sequenced genome into predicted positions within the gaps of a genome with a lower quality assembly. (Scaffold filling, contig fusion and comparative gene order inference, A Muñoz, C Zheng, Q Zhu, VA Albert, Steve Rounsley and D Sankoff, BMC Bioinformatics 2010)
Plant Genomes
List of sequenced plant genomes with their corresponding published paper and genome sequence in CoGe.