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ID1      ID2      dN     dS     Omega   Label_ID1       Label_ID2     
+  Group
AVP78042 AVP78031 0.0059 0.1188 0.0500  SARSr-bat-CoV   SARSr-bat-CoV 
+  Intra
ATO98108 AVP78031 0.1373 1.4673 0.0936  SARSr-bat-CoV   SARSr-bat-CoV 
+  Intra
ATO98108 AVP78042 0.1371 1.4224 0.0964  SARSr-bat-CoV   SARSr-bat-CoV 
+  Intra

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Distance    ID_1        ID_2        Value
DISTANCE    AVP78042.1  ATO98108.1  0.29731
DISTANCE    AVP78042.1  ATO98120.1  0.29281
DISTANCE    AVP78042.1  ATO98132.1  0.33095

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use strict;
use warnings;
...
    load($file, \%table, $phase);
    $phase = 1 == @ARGV ? 'print' : '';
}

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ID1          ID2         dN          dS          Omega   Value   Label
+_ID1       Label_ID2       Group
AVP78042     AVP78031    0.0059      0.1188      0.0500 0.29731  SARSr
+-bat-CoV   SARSr-bat-CoV   Intra
ATO98108     AVP78031    0.1373      1.4673      0.0936    -     SARSr
+-bat-CoV   SARSr-bat-CoV   Intra