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SAPP

                                     The Life of Trees     (Or:  Still Another Phylogeny Program)

Inputs (SNPTree tool)

The SNPTree tool is a separate tool from SAPP (so it’s not directly related to the /SNPTREE section of the SAPP input file; they just happened to have the same name which in retrospect was probably a poor choice!).   However the formats used in this SNPTree tool are separate and completely different from the /SNPTREE section of the SAPP Text input file.  

Since the SAPP tool relies heavily on its internal database of SNP haplogroups and essentially has its own haplotree, users may find it useful to occasionally “look” at this internal haplotree.  This allows you to not only confirm that the SNPs you care about are included, but also allows you to see the current structure of the internal haplotree in case you DO want to override this or add to it within your SAPP Text file input that you provide to the SAPP tool.  Or you can also just use it to make pretty pictures of portions of the overall haplotree.  

The usual input to the tool is simple:  enter a SNP and if that SNP is found in the internal haplotree database, the SNPTree tool will produce a formatted tree structure showing the branches from that SNP down to present day.  Please see the Outputs page for a description of the output tree and other formats.

SNPs should be entered without major haplogroup designations, so enter “U106” instead of “R-U106”, since that ensures the SNP will be found regardless of which major haplogroup it’s in.   However if you DO enter a SNP in the format “R-U106”, the tool will check the major haplogroup designation and will flag as a warning if you’ve entered the wrong major haplogroup compared to where the SNP is located in the internal haplotree.  

Other input formats have been developed over time as follows.  In the descriptions below, <SNP> is used as a placeholder for any SNP name, like U106, Z3006.2, etc; which can optionally be entered with the major haplogroup designator as well.  

<SNP>   if found in the internal database, SNPTree will draw the haplotree branches as a PNG file from this SNP down to present day.

<SNP> <SNP>…   if more than one SNP is entered, SNPTree will look for the lowest connecting point on the haplotree for all SNPs entered (assuming they exist in the database) and will draw the haplotree branches as a PNG file ONLY from that connecting SNP down to the SNPs entered.

<SNP> <SNP>… FULL   as above but adding the keyword “FULL” will cause SNPTree to additionally draw the branches from each SNP entered down to present day.  

<SNP1> ONLY <SNP2>  using the keyword ONLY will cause SNPTree to draw only the branch from <SNP1> to <SNP2> and then all branches from <SNP2> down to present day.  

<SNP1> FLAG <SNP2> <SNP3>…   SNPTree will draw the haplotree starting from <SNP1> down to present day, and IF the SNPs listed after the ‘FLAG’ keyword exist in those branches it will highlight those SNPs as yellow nodes.

<SNP> FIND   If the ‘FIND’ keyword is entered SNPTree will not produce an output tree but will simply search its internal database and produce a list of SNPs that match the input SNP provided (both exact matches and partial matches are reported separately).  

The following keywords can also be added at the end of the input string.

… MAJORS   If the keyword ‘MAJORS’ is added at the end of the input, SNPTree will add the major haplogroup designator in the SNP nodes of the output PNG tree (so R-U106 would be shown rather than U106, etc).  

… TITLE   If the keyword “TITLE” is added, SNPTree will add the input string to the output PNG file as a title.  

… LARGER   if this keyword is used, SNPTree will change the parameters of the output PNG tree to try and show larger SNP nodes for easier readability.  Note that with larger trees this can cause more overlap between SNP nodes, resulting in LESS readability.  

… YELLOW   if this keyword is used, SNPTree will make ALL SNP nodes on the output PNG tree yellow instead of the default green.

… LIMIT n   Usually if the number of SNP nodes is too large to fit on one page, SNPTree will automatically prune the more recent branches of the haplotree to show only the number of SNPs below the SNP entered which can fit on a page.  Use of the “LIMIT” keyword along with a number of SNPs allows you to adjust the output PNG tree to only display branching up to that number of SNPs below the “root” SNP.  Note that this may cause SNP nodes to overlap in the lower branches of the PNG tree.  

… NOCUT   this keyword causes SNPTree to not limit the output PNG tree but attempt to display ALL SNP nodes from the SNP entered.  This should be used sparingly since the output PNG file can easily become too large to be readable or of an unmanageable file size.  

… NEWICK   This keyword will cause SNPTree to not produce an output PNG tree but instead produce the same tree in a TXT file in standard NEWICK format.  This can be then imported into various other tools that can draw and manipulate Newick trees (like the ITOL, Interactive Tree of Life).  

… NODEXL   This keyword will cause SNPTree to not produce an output PNG tree but instead produce the same tree in a TXT file which can be imported into the NODEXL Excel tool.  

    SNPTree:     Inputs    Outputs