Why can some Sanger ab1 files not be read? Is there an alternative, if the base-called sequence is missing (PBAS tag)?

If the sequencer used to generate the ab1 files is Applied Biosystem 3130XL / ABI3130XL:

To load a Sanger file, AlamutTM Visual Plus uses the “PBAS” tag of the ABIF format. The “PBAS” tag contains the base-called sequence (i.e the nucleic sequence identified from the electropherogram).

Applied Biosystem 3130XL / ABI3130XL sequencer does not do the base calling step. In that case, sequence analysis software has to be used to do the base calling and to generate a Sanger file compatible with AlamutTM Visual Plus.

See here for more info about the ABIF format: https://projects.nfstc.org/workshops/resources/articles/ABIF_File_Format.pdf