non continuous characters in output

[pwkooij]

I ran PICS-Ord on several ambiguous regions in my alignment and tried to analyse all in partitions with RAxML. However, RAxML gave the following error

Multi State Error, characters must be used in the order they are available, i.e. 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V You are using the following characters: 0 2 3 4 5 6 9

It seems that at least one of my recoded regions is not continuous, i.e. missing 1 7 and 8, and RAxML doesn't accept that. Is there a way to correct this?

[reedacartwright]

I think the easiest solution is to remap the characters in your alignment so that 0 2 3 4 5 6 9 becomes 0 1 2 3 4 5 6.

[pwkooij]

I thought it would be ok to do so, so I did that by hand (i.e. find/replace) in a text editor. Any program that can do that more easily.

Also, would it be possible to have PICS-Ord avoid creating that?

[reedacartwright]

I'll see if I can get a student to figure out a fix.

[pwkooij]

Thanks, hope you can find one! And thanks for the information