multiple-files: No

Analysis Description
--------------------
RELAX (a random effects test of selection relaxation) uses a random
effects branch-site model framework to test whether a set of 'Test'
branches evolves under relaxed selection relative to a set of
'Reference' branches (R), as measured by the relaxation parameter (K).
Version 2.1 adds a check for stability in K estimates to try to mitigate
convergence problems. Version 3 provides support for >2 branch sets.
Version 3.1 adds LHC + Nedler-Mead initial fit phase and keyword
support. Version 3.1.1 adds some bug fixes for better convergence.
Version 4.0 adds support for synonymous rate variation. Version 4.1 adds
further support for multiple hit models. Version 4.1.1 adds reporting
for convergence diagnostics. Version 4.5 adds support for multiple
datasets for joint testing.

- __Requirements__: in-frame codon alignment and a phylogenetic tree, with at least two
groups of branches defined using the {} notation (one group can be
defined as all unlabeled branches)

- __Citation__: RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015).
Mol Biol Evol 32 (3): 820-832

- __Written by__: Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM /
UCSD viral evolution g

- __Contact Information__: spond@temple.edu

- __Analysis Version__: 4.5


>code => Universal
/home/datamonkey/datamonkey-js-server/production/app/relax/output/67ce93bbc7c3b6a8ab8185b6.tre
/home/datamonkey/datamonkey-js-server/production/app/relax/output/67ce93bbc7c3b6a8ab8185b6.tre

>Loaded a multiple sequence alignment with **42** sequences, **752** codons, and **1** partitions from `/home/datamonkey/datamonkey-js-server/production/app/relax/output/67ce93bbc7c3b6a8ab8185b6`
Error:
RELAX requires at least one designated set of branches in the tree. in call to assert(AYtyGOjN.option_count>=2, error_msg);

Function call stack
1 :  assert(AYtyGOjN.option_count>=2, error_msg);

	Keyword arguments:
		{
		 "kill-zero-lengths":"No",
		 "mode":"Classic mode",
		 "models":"All",
		 "output":"/home/datamonkey/datamonkey-js-server/production/app/relax/output/67ce93bbc7c3b6a8ab8185b6.RELAX.json",
		 "rates":"3",
		 "reference":"REFERENCE",
		 "test":"TEST"
		}
-------
2 :  ExecuteCommands("assert (`statement`, error_msg)", /home/datamonkey/datamonkey-js-server/production/app/relax/../../.hyphy/res/TemplateBatchFiles/libv3/);

	Keyword arguments:
		{
		 "kill-zero-lengths":"No",
		 "mode":"Classic mode",
		 "models":"All",
		 "output":"/home/datamonkey/datamonkey-js-server/production/app/relax/output/67ce93bbc7c3b6a8ab8185b6.RELAX.json",
		 "rates":"3",
		 "reference":"REFERENCE",
		 "test":"TEST"
		}
-------
3 :  [namespace = AYtyGOjN] io.CheckAssertion("`&option_count` >= 2","RELAX requires at least one designated set of branches in the tree.");

	Keyword arguments:
		{
		 "kill-zero-lengths":"No",
		 "mode":"Classic mode",
		 "models":"All",
		 "output":"/home/datamonkey/datamonkey-js-server/production/app/relax/output/67ce93bbc7c3b6a8ab8185b6.RELAX.json",
		 "rates":"3",
		 "reference":"REFERENCE",
		 "test":"TEST"
		}
-------
4 :  [namespace = relax] selected_branches=Call(settings[utility.getGlobalValue("terms.settings.branch_selector")],partitions_and_trees);

	Keyword arguments:
		{
		 "kill-zero-lengths":"No",
		 "mode":"Classic mode",
		 "models":"All",
		 "output":"/home/datamonkey/datamonkey-js-server/production/app/relax/output/67ce93bbc7c3b6a8ab8185b6.RELAX.json",
		 "rates":"3",
		 "reference":"REFERENCE",
		 "test":"TEST"
		}
-------
5 :  [namespace = relax] load_file({utility.getGlobalValue("terms.multiple_files"):multiple_files,utility.getGlobalValue("terms.prefix"):"relax",utility.getGlobalValue("terms.settings"):{utility.getGlobalValue("terms.settings.branch_selector"):"relax.select_branches"}});

	Keyword arguments:
		{
		 "kill-zero-lengths":"No",
		 "mode":"Classic mode",
		 "models":"All",
		 "output":"/home/datamonkey/datamonkey-js-server/production/app/relax/output/67ce93bbc7c3b6a8ab8185b6.RELAX.json",
		 "rates":"3",
		 "reference":"REFERENCE",
		 "test":"TEST"
		}
-------
6 :  namespace 

Step 0.LoadFunctionLibrary("modules/shared-load-file.bf", /home/datamonkey/datamonkey-js-server/production/app/relax/../../.hyphy/res//TemplateBatchFiles/SelectionAnalyses/);

Step 1.load_file({utility.getGlobalValue("terms.multiple_files"):multiple_files,utility.getGlobalValue("terms.prefix"):"relax",utility.getGlobalValue("terms.settings"):{utility.getGlobalValue("terms.settings.branch_selector"):"relax.select_branches"}});

Step 2.LoadFunctionLibrary("modules/grid_compute.ibf", /home/datamonkey/datamonkey-js-server/production/app/relax/../../.hyphy/res//TemplateBatchFiles/SelectionAnalyses/);;

	Keyword arguments:
		{
		 "kill-zero-lengths":"No",
		 "mode":"Classic mode",
		 "models":"All",
		 "output":"/home/datamonkey/datamonkey-js-server/production/app/relax/output/67ce93bbc7c3b6a8ab8185b6.RELAX.json",
		 "rates":"3",
		 "reference":"REFERENCE",
		 "test":"TEST"
		}
-------