Re: [graphviz-interest] Dendrograms/Cladograms

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Hi Herman

On 26/12/15 12:20, [email protected] wrote:
> Hi,
>
>> o Write all code in Perl. This is my strong preference.
>>
> graph traversal can be done in any language including PERL.

The name is 'Perl'.

>> o Avoid calling any external software if possible. This is to simplify
>> end-user usage.
>>
> You will call dot -- what is the difference to calling pic?

Not much, except of course my bias.

>> o If calling external software, stick to formats I'm familiar with.
>> So, DOT language in preference to .pic.
>>
> But all answers in this thread told you that your rectangular cladogram
> drawings cannot be done with dot, neither with nor without "splines=ortho".

Exactly. That's why I've almost finished my new Perl module.

> Is it correct that you do not have sample inputs for your cladograms yet?
> Without sample inputs no algorithm can be developed, regardless of
> programming or layout tool/language.

See attached! It contains 2 sample files, and some comments.

The file format is something I invented for use be the new code.

-- 
Ron Savage - savage.net.au

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	Sample 1:

	See L<https://en.wikipedia.org/wiki/Cladogram>

			+---- Beetles
			|
			|
	Root ---+	+---- Wasps, bees, ants
			|	|
			|	|
			1---+	+---- Butterflies, moths
				|	|
				|	|
				2---+
					|
					|
					+---- Flies


	Parent	Place	Node
	root	above	Beetles
	root	below	1
	1		above	Wasps, bees, ants
	1		below	2
	2		above	Butterflies, moths
	2		below	Flies

	Sample 2:

	See L<http://phenomena.nationalgeographic.com/2015/12/11/paleo-profile-the-smoke-hill-bird/>

			+--- Archaeopterix lithographica
			|
			|
			|
	Root ---+	+--- Apsaravis ukhaana
			|	|
			|	|
			|	|
			1---+	+--- Gansus yumemensis
				|	|
				|	|
				|	|
				2---+	+--- Ichthyornis dispar
					|	|
					|	|		+--- Gallus gallus
					|	|		|
					3---+	5---+
						|	|	|
						|	|	+--- Anas clypeata
						|	|
						4---+
							|	+--- Pasquiaornis
							|	|
							|	|
							6---+	+--- Enaliornis
								|	|
								|	|
								|	|
								7---+	+--- Baptornis advenus
									|	|
									|	|		+--- Brodavis varnei
									|	|		|
									8---+	10--+
										|	|	|
										|	|	+--- Brodavis baileyi
										|	|
										9---+
											|	+--- Fumicollis hoffmani
											|	|
											|	|
											11--+	+--- Parahesperornis alexi
												|	|
												|	|
												12--+
													|
													|
													+--- Hesperornis regalis

	Parent	Place	Node
	root	above	Archaeopterix lithographica
	root	below	1
	1		above	Apsaravis ukhaana
	1		below	2
	2		above	Gansus yumemensis
	2		below	3
	3		above	Ichthyornis dispar
	3		below	4
	4		above	5
	4		below	6
	5		above	Gallus gallus
	5		below	Anas clypeata
	6		above	Pasquiaornis
	6		below	7
	7		above	Enaliornis
	7		below	8
	8		above	Baptornis advenus
	8		below	9
	9		above	10
	9		below	11
	10		above	Brodavis varnei
	10		below	Brodavis baileyi
	11		above	Fumicollis hoffmani
	11		below	12
	12		above	Parahesperornis alexi
	12		below	Hesperornis regalis

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