'.' is frequently used as gap character. Should be easy to add: https://github.com/wash/rnacode/blob/fe20868df016f3be20351bcbdcecd89cb4d65003/phyml/utilities.c#L4484 and here https://github.com/wash/rnacode/blob/fe20868df016f3be20351bcbdcecd89cb4d65003/phyml/utilities.c#L4521 Error output is currently also not very helpful: `Unknown character state : �`