phyling - v2.3.0

Added

• The argument "seqtype" to SeqFileWrapperABC and its subclasses, which allow users to manually assign the seqtype of the inputs if the autodetection failed.

• The argument "seed" to tree module providing control to random generator during tree building.

Removed

• Tree displaying at the end of the tree module.

Changed

• Swap the key-value in DataListABC checksums which allow to look up using input checksums instead of input names.

• Use hierarchical loggers to better control the logging behavior. Now core modules (align, filter, tree) will output logs to a file [output_dir]/log.txt.

Fixed

• The order of the checksums in HMMMarkerSet generated from different platforms (x86 Linux and M series macos) are different.

• Error when estimating the threads during the align module with only 1 job.

• Error message traceback issue when monitoring the progress with progress daemon.

- Python
Published by github-actions[bot] 7 months ago

phyling - v2.2.0

Changed

• Use JC instead of GTR for faster phylogenetic inference during filtering step.

• Swap back to FastTree since VeryFastTree stuck occasionally. #35

• Enable --noml option for FastTree during filtering step by default. Users can use --ml in filter module to enable it.

• The hmmsearch step now report only single hit instead of the top hit of each markers. Therefore the final results will be single-copy orthologs.

• Use the fractional process indicator in search, filter and tree modules to better monitor the run.

• Move the tree construction comments from the top of the newick file to log.txt to avoid newick file loading failure in some of the software.

Fixed

• Fix guess_seqtype failure when having ambiguous codes in input sequences.

- Python
Published by github-actions[bot] 10 months ago

phyling - v2.1.1

Changed

• Set HMM.name to the filename of the hmm profile to adapt the change on the v12 dataset.

Fixed

• The treeness/RCV computation error when the tree's total branch length is zero.

- Python
Published by github-actions[bot] 11 months ago

phyling - v2.1.0

Added

• Environment variable PHYLING_DB that can be set to retrieve the database across multiple paths.

• Site concordance factor along with bootstrap value to better interpret branch support.

Removed

• The threads option in SearchHitsManager load method - it run faster in single process/thread.

• Custom bootstrap value assignment in main menu. Now bootstrap was done by UFBoot with 1000 replicates, standardized across all tools.

Changed

• Make SampleList hashable and use it directly in SearchHits instead of just name.

• Remove the selected_MSAs folder and directly link the selected MSAs to the main output folder produced by the filter module.

• Use VeryFastTree to replace FastTree.

• In consensus mode, use GTR and LG models for DNA and peptide data. In concatenation mode, use ModelFinder to find the best model(s)

• Use UFBoot for bootstrapping after tree building by either tool.

Fixed

• The unload data when hmmsearch with multithreads.

• The FileNotFoundError when rerun in a different working directory.

• The missing newline of the treeness file output from filter module.

• Simplify the log when verbose is disabled.

- Python
Published by github-actions[bot] 12 months ago

phyling - v2.0.0

Added

• phyling download list now will also print out the markersets that have already been downloaded.

• The filter module that calculate the treeness/RCV scores through PhyKIT to filter the uninformative markers. Use -n/--top_n_toverr to specify the number of markers you which to use in the final tree building.

• RAxML-NG and IQTree are now available for final tree building.

Removed

• Output option in download module. Now all the BUSCO datasets will be saved in the config folder ~/.phyling/HMM.

• Remove --from_checkpoint feature. Output to the previous output folder will trigger the check and automatically determine the rerun status.

• Remove tree building methods UPGMA and Neighbor Joining.

Changed

• Change the align module -m/--markerset behavior. It firstly searches against the given path and the config folder ~/.phyling/HMM if the path doesn't exist. Users can also directly specify the markerset name that has already been downloaded and saved in the config folder.

• Use timestamp for default output folder in align and tree module.

• Use FastTree to replace the UPGMA for the default tree building method.

Fixed

• Fix the multiprocessing issue.

- Python
Published by github-actions[bot] about 1 year ago

phyling - v2.0.0-beta

Changed

• Use ClipKIT to replace the self-defined function for trimming off the sites that display poor phylogenetic signal.
• Move the MSA concatenate function from align module to tree module. Users who want to try different tree building strategy won't have to rerun the align module again.
• Replace the VeryFastTree with FastTree for stability.

Added

• Check for duplicated sample names.
• Report problematic cds sequences.
• Use checkpoint file to save the hmmsearch results to prevent rerunning the search process when adding/removing samples.

Fixed

• Fix the bug caused by translation from cds sequences with invalid length.
• Fix the bug caused by inconsistent MSA output extension.
• Fix the bug that the trimming function always return peptide MSA if the sequence has no site being trimmed.
• Fix the Python logger issue.

- Python
Published by github-actions[bot] over 2 years ago

phyling - v0.9.0

- Python
Published by chtsai0105 over 2 years ago

phyling - v1.1beta Intermediate release

Archive of current code for citation and release, but there are revisions still in progress. Included a CITATION.cff file and some of the framework for BUSCO marker set use direct from unannotated genomes.

- Python
Published by hyphaltip almost 3 years ago