Anyone tell you they'd appreciate a PowerPoint presentation on your stories? 😂 (thanks LibreOffice) You'll catch me on stream fiddling with this (which btw I'll be streaming more likely until April due to *circumstances*) #Phyx

Day 29: Owl / Yearning ~ Sometimes camping is about the experience, and other times it's necessity... for some it's enjoyment #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 26: Pillow / Burning ~ Cultural differences are fun! Look up Chinese/ancient pillows! It's a history rabbit hole #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 22: Mine / Feast ~ Nothing like a business celebration! #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 21: Fragile / Hand ~ Deer vs crow #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 18: Patrol / Jealousy ~ Catching up! #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 16: Retired / Lie ~ Family dynamics are fun! Shockingly first parent-child interaction I've done for this series, whoops. #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 15: Island / Rip ~ Every JRPG needs a lizard people race! Bringing in a character from another project (We'll see if the race name sticks) #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 14: Prison / Mirror ~ scene in a nutshell: rich kids vs street rat #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 12: Cough / Window ~ Gotta set up the ship so it can sail! #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 11: Song / Arcade ~ Be fun to see how much this scene changes when I revisit it. Especially figuring out when things take place as that changes who's present #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 9: Path / Scar ~ The brothers can be lovingly chaotic, which means teasing for their companions as well #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 8: Resignation / Artificial ~ Not at all inspired by a certain manga/anime series regarding homunculi and chimeras... #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 7: Shrine / Treasury ~ Nothing like a Call to Adventure! #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx
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Day 6: Euphoria / Deck ~ Featuring a familiar face! My friend @fruitloopchan.bsky.social and I like to cameo each other's Ocs, check out our co-authored story: Time Zero: Secret of the Gods! #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing #Phyx

Day 4: Tunnel / Hairstyle ~ Not everyone has a good sibling relationship in #Phyx. Know someone like this? #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing

Day 3: Backstab / Camp ~ Feeling out character interactions a bit more for #Phyx. If it helps, Chira's voice claim is Jinx (Arcane) and Leif's is Gus/Sweet Tooth 🤭 #NovNov #Novelember #writingcommunity #Novelemberprompts25 #Novelember2025prompts #writing

Release v1.3.2 · FePhyFoFum/phyx pxbp works! Tons of tiny fixes.

Gnu #phyx release for those who celebrate. A slew of tiny fixes since the last release github.com/FePhyFoFum/p... #phylogenetics 🧪

GitHub - FePhyFoFum/phyx: phylogenetics tools for linux (and other mostly posix compliant) computers phylogenetics tools for linux (and other mostly posix compliant) computers - FePhyFoFum/phyx

Anyway, _we_ have found #phyx to be super useful and convenient (I think we all use it every day). Maybe you will too? Any ideas for new programs, feature requests, or bug reports can be submitted to our github page https://github.com/FePhyFoFum/phyx Thanks!

Is that all? Nope! #phyx currently consists of some 40 programs, and is continually growing. And what is more, because phyx works on stdin/stdout, programs can be piped to one another to build custom pipelines.

#phyx has some simulation capabilities as well. To simulate a number (-n) of birth-death trees, use `pxbdsim` (complementary, bd models can be fit using `pxbdfit`). Sequences can be simulated with `pxseqgen`.

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants - BMC Ecology and Evolution Background The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in one of several ways: by binning gene regions into subsets to isolate consistent phylogenetic signal; by using gene-tree methods for reconstruction, where conflict is presumed to be explained by incomplete lineage sorting (ILS); or through concatenation, where noise is presumed to be the dominant source of conflict. The results provided herein emphasize that analysis of individual homologous gene regions can greatly improve our understanding of the underlying conflict within these datasets. Results Here we examined two published transcriptomic datasets, the angiosperm group Caryophyllales and the aculeate Hymenoptera, for the presence of conflict, concordance, and gene duplications in individual homologs across the phylogeny. We found significant conflict throughout the phylogeny in both datasets and in particular along the backbone. While some nodes in each phylogeny showed patterns of conflict similar to what might be expected with ILS alone, the backbone nodes also exhibited low levels of phylogenetic signal. In addition, certain nodes, especially in the Caryophyllales, had highly elevated levels of strongly supported conflict that cannot be explained by ILS alone. Conclusion This study demonstrates that phylogenetic signal is highly variable in phylogenomic data sampled across related species and poses challenges when conducting species tree analyses on large genomic and transcriptomic datasets. Further insight into the conflict and processes underlying these complex datasets is necessary to improve and develop adequate models for sequence analysis and downstream applications. To aid this effort, we developed the open source software phyparts ( https://bitbucket.org/blackrim/phyparts ), which calculates unique, conflicting, and concordant bipartitions, maps gene duplications, and outputs summary statistics such as internode certainy (ICA) scores and node-specific counts of gene duplications.

Want to analyze the bipartitions found across trees à la Smith et al. (2015)? bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-... Use `pxbp`. #phyx

Here is an example from our supp. info.: combining tree logs of 2.6 GB each. Processing involved a burnin of 25% and thinning to every 10th sample. #phyx executed in a few seconds using only 600 KB of RAM while the alternatives used GBs of RAM and could take over an hour.

Dealing with large MCMC logs (parameters or trees) can be cumbersome. `pxlog` can burnin, thin, and combine multiple files. Because #phyx deals with streams, it is very memory efficient (only 1 sample is in memory at a time), and so can process many/large files.

#phyx has a tree cleaner: `pxcltr`. Can remove 2-degree nodes, internal node labels (support values or names), & root edges to generate a 'vanilla' newick representation. If you need to rescale your tree by a certain scaling factor (-s) or absolute root age (-r), use `pxtscale`.

Need to convert your in-frame nucleotide alignment to amino acids? `pxtlate` does that. To filter a fastq file by mean quality, use `pxfqfilt`. If you need to produce a bootstrapped or jackknifed alignment, `pxboot` is available. Concatenate with `pxcat`. #phyx

Sequence manipulation. Remove sites with too much ambiguous data (gap or N) with `pxclsq`. Or maybe you need to recode your nucleotide alignment; for that use `pxrecode`. Get a reverse complement with `pxrevcomp`. Generate a consensus sequence with `pxconsq`. #phyx

Need to do pairwise sequence alignment? #phyx has both Smith-Waterman (`pxsw`) and Needleman-Wunsch (`pxnw`) options.

#phyx has several programs for file format conversion. `pxs2fa`, `pxs2phy`, and `pxs2nex` will convert your alignment to fasta, phylip, and Nexus formats, respectively. Again, no need to specify incoming format. `pxt2new` will convert your tree to newick format.

Rooting (or unrooting) trees can be accomplished using `pxrr`. By default, rooting will by on the mrca of the outgroups provided (-g), _even_ if the group is not monophyletic. Alternatively, outgroups can be ranked (-r); rooting will be on the first found in the tree. #phyx