Epa Ng Versions Save

This is a version bump solely to fix a macOS compile error.

This version update primarily updates pllmodules and libpll, which, among other things, fixes a severe, silent issue that may occur with reference alignments that contain dots (.) as gap characters, as is the case with directly using the output from hmmalign.

For this reason we HIGHLY recommend updating to this newer release.

This minor update includes some QOL changes. BEWARE that if you update to this version via a git pull, you should also subsequently perform a git submodules update --init --recursive, as some dependecies have been updated along the way.

Interface changes:

• the --split function now also accepts fasta/fasta.gz files (Issue #28 )
• the --split function now produces a reference fasta file alongside the query file (and should now be more robust)

Features changes:

• node labels in the input newick string are now preserved in the output
• EPA-ng can now be installed using Conda
• improved the parsing of RAxML-8.x info files
• EXPERIMENTAL: added parsing of model parameters from iqtree log files

Code quality / bug fixes:

• added more safeguards to ensure that the reference tree is compatible with the reference MSA

This update introduces two bugfixes, one of which is related to the submodule genesis. Thus, if you want to update your existing clone of the repository, don't forget to git submodule update --init --recursive!

Bugfixes:

• a segmentation fault was resolved that occured with .bfast files of a size between 4MB and 8MB (issue #24)
• incorrect output ordering was resolved that has the (rare) potential of not outputting the placement with the highest LWR (issue #25)

As always, we strongly encurage you to update to the newest version.

This version fixes a result-breaking issue when calling EPA-ng with a rooted reference tree! This bug has existed since the intorudction of root preservation in v0.3.0. If you think you migth be affected, please update to v0.3.4!

Other minor changes/fixes:

• added an option to toggle rooting preservation
• fixed crash when trying to supply certain raxml8.info files via --model

Interface changes

• --model argument now also accepts raxml-ng .bestModel-type files
• added option to enable the use of rate scalers between automatic (default), on or off (--rate-scalers)
• --split now accepts interleaved phylip when parsing the reference file
• added an option to overwrite existing files (--redo)

Bugfixes

• fixed a small error in candidate selection that made it more agressive than intended
• fixed some missing include directives that caused the mac build to fail (thanks @gavinmdouglas!)
• fixed issue with reading files with windows line endings

Misc changes

• added some aliases on the command line to make usage more forgiving

This version fixes a fatal error in the MPI version (see issue #20).

Other minor fix: compile issue sometimes occuring under older GCC version (?)

WARNING This version has a fatal error in the MPI version, please use v0.3.2 instead!

EPA-ng now supports reading gzipped fasta files, automagic courtesy of @lczech 's genesis library!

Feature changes:

• reading from gzipped fasta files (e.g., fasta.gz) now possible

Bugfixes:

• fixed a compile issue from the last version with the MPI build
• fixed an issue with detection of OpenMP under clang/macOS
• extended the --precision changes from the last version to jpalce writing under MPI

Misc changes:

• updated pll-modules
• updated genesis (switch from custom feat/skipinput branch to master)
• refactored the distributed input code a bit (no more file skipping after reader creation)
• updated the version string properly this time

WARNING This version has a fatal error in the MPI version, please use v0.3.2 instead!

EPA-ng is now peer reviewed! Please cite the following paper when using it in your work:

Pierre Barbera, Alexey M Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomáš Flouri, Alexandros Stamatakis;
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences,
Systematic Biology, syy054, https://doi.org/10.1093/sysbio/syy054

This version introduces root preservation of the reference tree, compulsory specification of the model string/parameters, as well as some minor bug fixes and improvements. This is also the first verion I don't consider beta anymore, as the program has been very stable over the last months across multiple projects and datasets.

Interface changes

• --model parameter is now compulsory and works identically with the same option in raxml-ng
• added --precision argument to specify output floating point precision

Feature changes

• added a check to disallow multifurcations in the reference tree
• output floating point precision is now of uniform length (can be set via --precision)
• EPA-ng now preserves rooting, meaning that if you specify a rooted tree as the reference, that same tree will be the tree in the output. Unrooted trees are still used internally, but the placement results are translated to the rooted tree as they are written to file

Bugfixes

• added code to catch sequences that are all gap and fail when found
• fixed possible failure when empty work structures would have been merged
• fixed a bug where pll scalers were copied incorrectly
• fixed a bug sometimes leading to incorrect placement distal lengths

Misc changes

• switched to cmake build for pll/pll-modules
• improved some error messages
• added test data and link to test data used in the paper
• updated citation info

This release changes crucial values in bfast-files. If you use bfast, please re-convert them!

Bugfixes

• fixed multiple bugs with the bfast reader/writer
• updated genesis to fix possible race conditions