Mgcluster
From mothur
The mgcluster command ....
For this tutorial you should download the ..... file and decompress it.
Contents |
Default settings
The blast parameter is required...
mgcluster(blast=bap.100.blast)
Options
name
mgcluster(blast=bap.100.blast, name=bap.100.names)
method
- Nearest neighbor: Each of the sequences within an OTU are at most X% distant from the most similar sequence in the OTU.
- Furthest neighbor: All of the sequences within an OTU are at most X% distant from all of the other sequences within the OTU.
- Average neighbor: This method is a middle ground between the other two algorithms.
cluster method: furthest, nearest or average.
default = furthest
cutoff
default = 0.70 mgcluster(blast=bap.100.blast, cutoff=1.0)
precision
default = 100
merge
Default = true, meaning merge after clustering mgcluster(blast=bap.100.blast, merge=f)
min
default = true, meaning use minimum blast score ratio mgcluster(blast=bap.100.blast, min=f)
length
default = 5, minimum overlap
mgcluster(blast=bap.100.blast, length=10)
penalty
default = 0.10
mgcluster(blast=bap.100.blast, penalty=0.15)
hcluster
default = false, meaning don't use hcluster, use cluster.
mgcluster(blast=bap.100.blast, hcluster=t)
