* Update concept.rst
* Update input_output.rst
* Update usage.rst (file paths and descriptions)
* Delete .buildinfo
* Describe ks.tsv file format
* Add (E)LMM file format description; internal links
* Add (E)LMM file figures
* Rename header in ELMM TSV file
* Restructure mixture model section and add table
* Reduce paralog analyses description in docs
* Add Note block in input_output.rst about filenames
* Rename header in main.nf
* Add preprint DOI in "How to cite us" doc page
* Replace <focal species> with species (filename)

* Ks plot without divergence lines has inner legend
* Anchor cluster plot without lines has inner legend
* Exp-log plot without lines has inner legend
* Lognormal plot without lines has inner legend
* Reduce right margin of simple plots
* Ask matplotlib>=3.3.3 to fix a compatibility issue

* Anchor weights (also in paralogs-analyses command)
* Set the number of components to 3 in test dataset
* Rename function in anchor weighting
* Move compute_weight; del 0.05 in ks_list_from_tsv

* Rename with 'focal species'
Rename 'species of interest' and 'main species' in documentation RST files,
function docstrings, comments in code, in config_elaeis.txt, but also
in some actual code lines: in generate_config.py and fc_configfile.py
('focal_species' field), in main.nf (parse config file in setup process).

* renaming gff_filename field
* Rename (adjustment arrows, bootstrap iterations)
* Improve parameter description in configuration.rst
* Rename "adjustment" in filenames and python output
* Rename rates: branch contribution or ks distances
* Rename "adjustment" (leftover)

* Describe logging level in configuration.rst

* Add database names in input_output.rst

* Rename peak_stats
* Rename focal species in readme

* Catch missing species in fasta_filenames
* Catch missing species in latin_names and exit
* Bugfix for catch missing species in latin_names
* Bugifx to catch missing species in latin_names

* Rename max_mixture_model_ks

* Add parameter default values in configuration.rst

* Correct RST syntax

* Add output directory and filenames to docs

* Remove AIC and BIC PDFs

* Catching missing species WIP

* Remove unnecessary newick_tree variable

* Improve checking steps for FASTA and latin names.

Exit if latin_names is empty or one or more species are missing.
The new function check_complete_dictionary() lists the missing
species in latin_names and exits.

Check and warn if FASTA of GFF files are missing; exit after all
the files have been checked.

* Update test_pipeline.yml
* Update README.md

* Update doc/source/concept.rst
* Update doc/source/configuration.rst

* Update ksrates/fc_configfile.py

* Update doc/source/configuration.rst
* Update doc/source/paralogs_analyses.rst

* Update ksrates/correct.py
* Update ksrates/fc_rrt_correction.py

* Accept suggestions by reviewer about renaming

* Rename function "decompose_ortholog_ks"
* Rename function to check file content
* Rename function to check complete latin_names

* Removing comment about Nextflow in plot_tree.py

* Rename back to "species of interest" in wgd files

* Mention GFF file in "colinearity" config field

* Move logging message in setup_correction.py

* Rename "colinearity" to "anchors" in LMM filenames

* Change figure title of anchor Ks clustering picture

* Rename to "focal species" in readme

* Fix RST title

* Link to "paralogs analyses" from expert config

* Apply suggestions from code review

* Replace GFF dict with string; improve checkpoints

* Remove unnecessary function argument

Co-authored-by: cesen <cesen@psb.ugent.be>
Co-authored-by: lohausr <56632794+lohausr@users.noreply.github.com>

* Update config.rst: mainly Nextflow config section
* Apply suggestions from code review
* Fix wgdOrtholog dependencies; improve beforeScript
* Suggest threads/memory resources
* Update test_pipeline.yml

Co-authored-by: cesen <cesen@psb.ugent.be>
Co-authored-by: lohausr <56632794+lohausr@users.noreply.github.com>

Add bioRxiv citation and links