Ben Fulton
Ben Fulton
Per the mailing list, the command sequence > $ seed 100 > $ load -i filtered_Mollusks_only_Jan7_families.txt -t 8 -l log_Apr9_Mollusk_only_reg_p001_.txt -p 0.01 > $ tree ((((BG:138.0008395,LS:138.0008395):67.4885290,AC:205.4893684):217.5106316,LG:423.0000000):93.3000000,CG:516.3000000) > $ lambda -s...
It would be convenient to be able to generate families based just on a tree, a rootdist, and a lambda value.
Does the max_size option or the filter command keep track of which families are left out of the analysis? I think the reason I don't use the filter command is...
For example, if a script says "lambda search" instead of "lambda -s" the error message doesn't make sense. All commands should consistently throw exceptions if they are passed invalid arguments.
ERROR(tree.c): running infix on nonbinary tree (memory_new) Error in memory allocation: 12: Cannot allocate memory I pasted the tree into Seaview and it makes the tree without problem. (((((((A:109.5082649,B:109.5082649):83.2172160,C:192.7254808):262.8484741,D:455.5739549):87.4210709,E:542.9950258):373.0049742,(F:425.0000000,(G:346.0000000,(H:94.0000000,(I:6.8896471,J:6.8896471):87.1103529):252.0000000):79.0000000):491.0000000):405.4946417,K:1321.4946417)); Seems...
Allow providing a tree in the file as well so all parameters can be set with one file.
Maybe a table more like the input file, but this time with the internal nodes as columns as well? The individual cells could show the observed/inferred count and the change...
It would be interesting to implement the method Ane developed in Rabier et al. (2014). Ane has given permission and we need to make sure to give credit where due....
Installed this on my local machine and I really like it! Now I'd like to install it on a larger cluster where I don't have root access to install anything....