PhyloSift analysis of Deepsea OTUs

Prepping for lab meeting tomorrow, so looking at the results of the PhyloSift runs for the Deepsea OTU data.

Edge PCA (produces an .xml tree file) :

./guppy pca –out-dir ~/phylosift_v1.0.0_01/ ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_ShallowCalif.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_ShallowGulf.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic22.1.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic25.2.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic29.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic43.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic45.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific128.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific237.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific321.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific422.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific528.fna/treeDir/18s_reps.1.jplace –prefix guppyDS

Squash clustering (

./guppy squash –out-dir ~/phylosift_v1.0.0_01/ ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_ShallowCalif.fna/treeDir/ShallowCalif_18Sreps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_ShallowGulf.fna/treeDir/ShallowGulf_18Sreps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic22.1.fna/treeDir/Atlantic22.1_18Sreps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic25.2.fna/treeDir/Atlantic25.2_18Sreps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic29.fna/treeDir/Atlantic29_18Sreps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic43.fna/treeDir/Atlantic43_18Sreps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic45.fna/treeDir/Atlantic45_18Sreps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific128.fna/treeDir/Pacific128_18Sreps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific237.fna/treeDir/Pacific237_18Sreps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific321.fna/treeDir/Pacific321_18Sreps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific422.fna/treeDir/Pacific422_18Sreps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific528.fna/treeDir/Pacific528_18Sreps.1.jplace –prefix guppyDeepsea_squash

Kantorovich-Rubinstein Distance:

~/phylosift_v1.0.0_01/bin$ ./guppy kr –out-dir ~/phylosift_v1.0.0_01/ ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_ShallowCalif.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_ShallowGulf.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic22.1.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic25.2.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic29.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic43.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Atlantic45.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific128.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific237.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific321.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific422.fna/treeDir/18s_reps.1.jplace ~/phylosift_v1.0.0_01/PS_temp/QiimeSplit_F04_Pacific528.fna/treeDir/18s_reps.1.jplace -o guppy_Deepsea_KRdistance

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