Add more info to manual

[psathyrella]

placeholder

├── cluster0
│   ├── cluster_seqs.fasta
│   └── mcmciter100000_mcmcthin100_tuneiter5000_tunethin100_numrates4_seed0
│       ├── burninfrac0.0001_subsampfrac0.05: everything in this dir is an output file
│       │   ├── aa_naive_seqs.dnamap: complements the .fasta file, has dna sequences
│       │   ├── aa_naive_seqs.fasta: aa naive sequences with probabilities (should match up with numbers from linearham_run.log)
│       │   ├── aa_naive_seqs.png: logo plot of of per-site aa naive sequence uncertainties corresponding to .fasta
│       │   ├── linearham_run.ess: unimportant
│       │   ├── linearham_run.log: each line is one sample. Ignore log likelihoods, treat each line as equal probability. (the log probs are for the distributions that were sampled from to *get* the lines in these files, i.e. ignore them)
│       │   ├── linearham_run.trees: each line is one sample.  Ignore log likelihoods, treat each line as equal probability.
│       │   └── seedseqQA013.2-igh: for each seed sequence we have a aa_lineage_seqs file, which is analagous to aa_naive_seqs in parent dir
│       │       ├── aa_lineage_seqs.dnamap: includes same naive seq stuff as in parent dir, as well as similar stuff for intermediate ancestors (except ignore probs for intermediates, since there isn\'t an easy way to compare them)
│       │       ├── aa_lineage_seqs.fasta: corresponds to dnamap
│       │       ├── aa_lineage_seqs.pfilter0.01.dot: each is a naive to seed lineage plot with the indicated probability threshold (threshold means we ignore potential ancestor chains/lineages less than that prob)
│       │       ├── aa_lineage_seqs.pfilter0.01.png
│       │       ├── aa_lineage_seqs.pfilter0.02.dot
│       │       ├── aa_lineage_seqs.pfilter0.02.png
│       │       ├── aa_lineage_seqs.pfilter0.04.dot
│       │       ├── aa_lineage_seqs.pfilter0.04.png
│       │       ├── aa_lineage_seqs.pfilter0.06.dot
│       │       ├── aa_lineage_seqs.pfilter0.06.png
│       │       ├── aa_lineage_seqs.pfilter0.08.dot
│       │       └── aa_lineage_seqs.pfilter0.08.png
│       ├── lh_revbayes_run.trees: ignore this file (the annotations seemed to not be self-consistent)
│       ├── revbayes_run.log
│       ├── revbayes_run.rev
│       ├── revbayes_run.stdout.log
│       └── revbayes_run.trees
├── partis_run.stdout.log
├── partis_run.yaml
└── run_qa013_synth_v19_1final.sh

[eharkins]

@dunleavy005 updated the readme and I just re-formatted to break it up a bit so closing this for now.