FAQ

1. What does PID stands for? 
• PID stands for Percent Identity and it implies the particular Manxcat run used (1 - PID) value of each aligned pair of sequences as the distance between the two original sequences corresponding to that particular pair. 
• See more on different distance types at DistanceTypes
2. What is Simple Points file?
• Given the input sequence file used in the particular Manxcat run, the Simple Points file presents 3D coordinates for each sequence in order. These coordinates are computed by the Manxcat program with its best effort to preserve the original distance between each pair. The term original distance refers to the distance (transformed distance if specified - see Distances and Transformations) calculated through aligning the corresponding two sequences.
• Note. In cases where Blast is used to do the alignment it's possible not to get alignments for certain sequence pairs. In such cases Manxcat may not produce coordinates for all the sequences. Therefore you may find some point numbers are missing in the Simple Points file although they are ordered by the point number. The value of the Distance Cut may also ignore pairs of sequences having a distance value greater than that, resulting similar missing points in the output. 
3. How do the coordinates in Simple Points correspond to COG clusters?
• Predefined cluster assignment is available for each sequence in the used set of COG sequences. These are available in the Introduction page.
4. What is the difference between COG95672 and COG50000? 
• COG95672 stands for the unique sequences filtered from the original set of sequences. It has 95672 sequences.
• COG50000 stands for the first 50,000 sequences taken out of the unique sequences file.
• Also note both these files preserve the same order as in the original set of sequences. In other words the sequences are not randomized.
5. Can you please give more details on distance transformations, i.e. Transformation: TM10,TP4 ?
• Please refer to the separate post on Distances and Transformations
6. What does DistanceCut: 0.96 mean?
• Please refer to the separate post on Distance Cut
7. Is PlotViz available for Linux?
• Currently, PlotViz is available for Windows and Mac environments only.
8. What are the selected clusters?
• Please refer to the separate post on The Role of Seven Clusters