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[diekhans]

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[robertopisa]

Dear Hal developers/maintainers, I have installed and used HAL suite for some analyses on Cactus output in multiple genomes alignment. I am a bit puzzled by the output format of hal- programs: where is it possible to find a detailed explanation of which values are stored in the various columns and how these values are computed? Thank you a lot!

[glennhickey]

The documentation I'm aware of is

• hal paper
• hal readme
• hal section in cactus readme

If you have a specific question that's not covered above, you can try asking it here.

[robertopisa]

Thank you very much for your prompt answer. Unfortunately, I had already checked this documentation: I found in there no explanation about, for instance, what the column "NumSequences" in halStats output files is recording and why it contains an integer larger than 1 only when the referring genome is an ancestor one. The documentation you cited does not contain an explanation of the various output files produced by hal-routines, or, at least, I was unable to find it.

[glennhickey]

In HAL each "genome" is a collection of "sequences", a general term for chromosomes or scaffolds or contigs depending on the input. Ancestral genomes may be broken into several sequences, even if input genomes have 1 each.

[robertopisa]

Got it, thank you. But is there a help file where I can find a detailed explanation of each field produced by hal-routines? the readme/help files are often explaining only how to use command line parameters, but they say nothing about the produced output. For instance, what is the meaning of GapDepletion? are they counted with respect to gaps in the current sequence or in the parent one? What I am looking for is a schema that, for each column of the output file of a given routine in the suite, explains what is the variable stored in there and how it is computed, possibly giving the used formula.