History of MBGD/Introduction/Phylogenetic_pattern_analysis (No. 3)

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MBGD Documents

Profile search†

Screen Explanation†

① Category(phenotype, environment information, taxonomy)
② List of items
③ List of genus
④ Presence organism box
⑤ Absence organism box
⑥ [Analyze] button

(a) If checked, only items that are common between the added items and items already in the presence organism box will remain.
(b) Add the item selected in List of genus to the Presence organism box.
(c) Clean up the Presence organism box
(d) Add to the Absence organism box what is not included in the Presence organism box
(e) Add the item selected in List of genus to the Absence organism box.
(f) Clean up the Absence organism box

Search flow†

1. Select category(phenotype, environment information, taxonomy) how to refine your organism
   
   
2. Selecting an item from the list will cause the corresponding genus to be selected
   
3. Select genus and place it in the Presence/Absence organism box
4. Click [Analyze] button
   

Category†

phenotype†

Select using phenotype information from gold

environment†

Select using environment information

taxonomy†

Select using taxonomy information

file†

file format
Comma Separated Format (genus name, value)
value 1= Add to presence organism box
value 0= Add to absence organism box
download sample.csv

Haloarcula,1
Halomicrobium,0
Halorhabdus,1
Halorientalis,0
Natronomonas,
Haloarculaceae,
Halalkalicoccus,

heder format

# G = 1   (convert "G" to 1)
# T = 0   (convert "T" to 0)
# 0.5 and above to 1
# 0.2 or less to 0
# between 0.3 and 0.4 to 1