-treelike signal into a tree. The inclusive ML-tree inference and EPA may, pending the gene-wise signal of the distinct tip, prefer a placement on an internal branch fitting the majority

If the signal in the matrix is trivial, the topology, or any > topological aspect that is > > trivial, > > > > will always be (nearly) the same irrespective of the

reason for poor Phytia scores in phylogenomic data is the general > low divergence between the genes that can be identified as homologues, but > more importantly that, especially

parameter-poor model (without variables in the case of JC) hinders RAxML from properly fit the model to the data and inviting branching artefacts, so-called "false positives

also because poor branch support is no criterion that you look at an evolutionary scenario like in the bottommost part: a fast radiating, widespread, genetically increasingly heterogenous

due to signal issues relating either to rogues ("jumping taxa", can include some that simply violate the principle of dichotomy), which is rather unproblematic, or poor

often the signal structure that > slows down the processing of such large data sets. There are two main > obstacles while roaming the tree-space (see also this paper on SARS-CoV

datasets with poor signal (many taxa > + few sites). So please let it run a bit longer. > > > > Best, > > Alexey > > > > On 24.12.20 16:53, Jeff Bowman wrote

Pending the signal structure in your alignment (and its size), a bootstrap resample may hence be completely devoid of discriminative characters or extremely biased by a few characters

of discriminate signal, being primitive, ie acting like an actual ancestor, incomplete lineage sorting issues, and being the product of reticulation). So, if you data is messy producing

handful of poor base calls (10 out of more than 15000 > variable sites potentially providing a phylogenetic signal) don't matter > for higher-level phylogenies, they are

because of poor > phylogenetic signal? > > > > Thanks! > > > > Miao > > > > > > Dr. Miao Sun > > Web: www.sunmiao.name Email: >

> diffuse signal and little overlap in the accessions" although the NGS > data is robust. The more noise you have in the data, the harder it will be to resolve the tree. >

to a signal issue. Moving this taxon, the rogue, may not change the overall likelihood of the tree. Hence, RAxML just picks one tree, even if it's a suboptimal one regarding character

the > signal in your data is not unambiguous, and then the best option is to use > a consensus network. For instance, you have A, B, and C all part of the > same subtree (clade in

Dear Gyozo, many thanks for sharing your solution! I just double-checked, and on our system (SLURM 18.08.4, CentOS 7.6.1810) both options - with and

> I've tried with --rate-scalers on using the failed run's starting tree and it seems to have gotten farther: > > [00:03:29 -

-treelike signal, so one would not search for just one tree. Consensus trees were helpful in the dawn of phylogenetics, when we only had parsimony (because distances were banned as

of phylogenetic signal on the inference in > RAxML? By 'sites > > >> with limited signal' I consider the following: > > >> > > >> 1