Comments (6)
@sbrobeson You can compile it with:
make pxssplit
The fact that it is not in the default list of programs to compile means that it might not be fully tested yet. It looks like it is one of mine, so I will take a look at it tomorrow. Sorry for the trouble. If this is something that you want to use, then processing your file(s)/commands(s) might help vet it.
from phyx.
Oof yeah this is not functional atm. I can get it working if that is what you need.
from phyx.
it would be great if you were able to get it working, thanks! it's not mission critical but having this would potentially speed up some processing steps for me in the future.
I am noticing the same problem with 'pxnni' if you are going in to fix parts of phyx. both make pxssplit
and make pxnni
work, but I cannot use them ("command not found").
from phyx.
The "command not found" message means you have compiled them, but not installed them. make install
will install any phyx program that has been compiled; i.e., you can call it from anywhere. Alternatively, you can call it locally by doing (for example) ./pxnni
(or using a path if you are not in the src directory).
I don't recall the details of how useful the NNI program is... I know at some point I had wanted it to generate all possible NNIs given a tree, but with no pressing use it fell through the cracks. In principle it is doable...
For pxssplit
we need to provide instructions for how the alignment is chopped up. I have been going back-and-forth with either a RAxML-type (i.e., 'modelfile')
DNA, mtDNA = 1-2066
DNA, CTYB = 1-1029
DNA, ND2 = 1030-2066
DNA, EEF = 2067-2990
DNA, GADPH = 2991-3406
DNA, HMG = 3407-4079
DNA, RHOD = 4080-5058
DNA, TGFb2 = 5059-5721
or NEXUS-type (i.e., CHARSETs)
CHARSET Full_mtDNA = 1-2066;
CHARSET CYTB = 1-1029; [1029]
CHARSET ND2 = 1030-2066; [1037]
CHARSET EEF = 2067-2990; [924]
CHARSET GADPH = 2991-3406; [416]
CHARSET HMG = 3407-4079; [673]
CHARSET RHOD = 4080-5058; [979]
CHARSET TGFb2 = 5059-5721; [663]
CHARSET Full_nuclear = 2067-5721; [3655]
although both will likely get implemented at some point. Is there one you prefer? I can get that one going first.
from phyx.
sorry for forgetting about this temporarily!
with regard to pxnni
, no problem, it's not something I personally need to use... just thought I would mention it as I found it as another non-working entry in the program list.
for pxssplit
I would probably favour the RAxML-type format, if only one can be prioritised. this isn't so urgent for me now as I slopped together a (less easy) workaround but may probably still be helpful for future alignment-rearranging.
from phyx.
That is how I am leaning as well, although this was put on the back burner. Thanks for letting me know your preference.
from phyx.
Related Issues (20)
- phylip gets corrupted when piped HOT 3
- a strange thing about pxrms program HOT 10
- pxtlate detects AA when DNA is present HOT 2
- duplicated species in clade groupings with pxbp
- How to install phyx on linux without root access ? HOT 5
- pxrlt and pxrls only change the final name on the list HOT 9
- pxrlt and pxrmt doesn't output tip name with "-" correctly HOT 5
- pxaa2cdn -r not working as expected HOT 8
- strange behavior with pxbp on computing cluster HOT 7
- pxcomp outputs an enormous file, or rejects unaligned sequences. HOT 6
- phyx installed HOT 11
- pxaa2cdn -r (again) HOT 10
- infinite loop in superdouble implementation with gcc 13 HOT 3
- Unable to ./configure HOT 4
- Debian 12 install, pxseqgen HOT 3
- autoconf error in installation HOT 5
- pxrms .txt file using wildcard HOT 6
- Phyx errot: double free or corruption (!prev) HOT 4
- GHA failing for mac (armadillo) 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 phyx.