Comments (4)
Whoops, sorry about that, I must've missed updating that bit of the docs for the switch to --get-selection-metrics (--get-tree-metrics is the old name for the same argument). I'll fix the docs but in the meantime you want to look here for a full description of the option: https://github.com/psathyrella/partis/blob/main/docs/subcommands.md#get-selection-metrics
from partis.
from partis.
Thank you for your response!
I am currently utilizing the fasttree for phylogenetic tree construction. During this process, I have observed a peculiar pattern where certain sequences are classified as nodes rather than leaves. These sequences are characterized by notably higher values of Local Branching Index (LBI) or Local Branching Ratio (LBR) compared to other samples in the dataset.
I want to know clarification on the criteria or algorithmic principles that Partis employs to designate certain sequences as nodes. Understanding the underlying rationale for this classification is crucial for the correct interpretation of my phylogenetic analysis results.
Additionally, I would appreciate any insights or guidelines on how to interpret these sequences that are identified as nodes. Are there specific biological or methodological implications associated with these sequences having higher LBI or LBR values?
Thanks.
from partis.
It's hard to be too definitive without seeing your particular data, but I can say that fasttree always puts all observed sequences as leaves. This I'm sure makes sense for its original use case, but as you're finding, observed BCR sequences are often internal nodes. Thus when partis is reading fasttree output, it collapses any leaves that are on zero-length branches (i.e. moves the observed sequence to the internal node at the top of the zero length branch). This is all fine, but you should know that if you're digging into the details of lineages and inferred ancestral nodes you might want to use a more accurate method like iqtree to double check results.
As to the LB metric values -- yeah they'll generally be much larger for internal nodes than leaf nodes, simply because leaf nodes have no descendents. There's more discussion in the paper (see screenshot for one bit), but the upshot is that while this is a heuristic, it's probably a reasonable one, and quite possible kind of close to optimal.
from partis.
Related Issues (20)
- Error in bcrham forward: sequences different length in Glomerator::NaiveHfrac HOT 10
- Fix super-long insertions/deletions in large, high-mutation families HOT 3
- Assertion error when annotating HOT 9
- Partis Killed - no other error message HOT 10
- AIRR output with paired-loci HOT 17
- disable germline inference HOT 7
- simulating paired chains HOT 13
- Add github actions HOT 1
- Fully switch to quay.io
- AIRR output crashes trying to call get_droplet_id HOT 5
- Mismatch between default and IMGT-aligned databases for macaques
- Dockerfile HOT 10
- KeyError when using --extra-annotation-columns HOT 2
- Docker container scipy versioning HOT 4
- Python version in docker: circle-plots.py HOT 25
- Table of contents entries for command line scripts in auto generated sphinx docs are confusing HOT 1
- Issues with COAR HOT 1
- Issue with annotate HOT 5
- Singularity HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from partis.