Hi, I have a new reference genome. And I intend to align it to reference genome of other related species, so as to determine the ancestral state for our reference genome. It's like genome alignment to genome. which tools can be used to achieve this? Thanks very much.
You want to do multiple genome alignments. There are many tools to do that -- MultiZ, and TBA from UCSC and Enredo-Peacan-Ortheus (EPO) from Ensembl are among the broadly used approaches.
You can look at Alignathon paper for many tools and comparisons. http://genome.cshlp.org/content/early/2014/10/01/gr.174920.114
Nice! Which one of these tools would allow me to reannotate the aligned genome? Like, I have a songbird genome ensemble still unpublished from a collaborator. This genome was mapped and annotated using a mix of stuff they did there. I want to align the ref falcon genome to this songbird genome and reannotate based on it. So that the positions correspond to each other. Tnxs