njrollins

Add alignment summary: organisms

1

Would be useful to give quick visual summary of what organisms are collected in the alignment. One option: represent aligned sequences in a tree or simply a bar-chart, colored by...

Include code developed in Toth-Petroczy 2016, recommend = include output and plot in Couplings stage, and contrast to 2ndary in PDBs in Compare stage

Add 'existing paired alignment' to complex pipeline

2

For some applications, such as protein-RNA complexes, I'd like to pair sequences by a custom method- and input already paired seqs (2 alignments where sequence X in ali 1 is...

Focus sequence non-functional if alphabet provided

1

When alphabet is specified, all sequence positions are modeled ignoring uppercase/lowercase Without alphabet ( assumes protein alphabet = a problem for RNAs ) ``` plmc -c my.model -f target_seq -t...

Cannot be installed on M1 or M2 Macs

4

Would be wonderful to update the code to be compatible with new Macs and any other devices incompatible with cuda. Currently does not install due to cudatoolkit and dgl, which...