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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.