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# Chimera check OCCURRENCE DESCRIPTION NOTES WARNINGS BUGS ## OCCURRENCE
### ARB_NT/Sequence/Chimera check
## DESCRIPTION
### Takes sequences, a tree and a column statistic as input, and generates a short sequence quality output string, which will be stored into the database under a user defined key. ### First the sequences are split into different slices: 2 pieces (front and back half) 5 equally sized pieces user defined pieces ### The programs sums up the weighted mutations for each sequence slice using a maximum likelihood technique. ### For each slice a students t-test (see http://en.wikipedia.org/wiki/T-test) is performed and its result is written into the XXX portions of the entries mentioned below. The t-test tests whether the likelyhood of a specific sequence slice (of one species) follows a t-distribution of the likelyhoods for that sequence slice in all examined species. ### The meaning of each X contains the result of the t-test (the "t-value") as follows: if the t-test succeeds the value of X is '1' up to '8' (where '5' is shown as '-'). if the t-test fails '0' or '9' is written to the X's if there is not enough data to perform the t-test, '.' is written to the X's ### Rule of thumb: Values near '0' or '9' indicate regions with an abnormal, values near '5' ('-') regions with a normal (i.e. expectable) number of weighted mutations. ### The sequence quality string written into a user-definable species field has the following format: MED SUM aXX bXXXXX cXXXXX...XXXX where: MED is the median of all t-values (0.0 = normal; <5.0 = succeeds t-test (mean); >5.0 = abnormal) SUM is the sum of all t-values aXX shows the quality for 2 pieces bXXXXX shows the quality for 5 pieces cXXXXX...XXXX shows the quality for user defined slices ### Optionally a 'quality' entry may be written to the alignment, allowing to display it in EDIT4 below the sequence. That quality entry simply is a "blown up" version of the "cXXXXX...XXXX" part of the sequence quality field.
## NOTES
### Only sequences which are in the tree are used. ### Slices in high variance regions more easily pass the t-test. ### Slices from sequences with higher overall variance more easily pass the t-test.
## WARNINGS
### Needs a really lot of computer memory!
## BUGS
### Does not delete the destination field of species not in the tree.