The Phylogenetic Handbook edited by Lemey et al. has a good introduction that covers the basics of molecular phylogenetics.

i think "The Phylogenetic Handbook" very good book for learning  phylogeny, where all major aspects included.  i start learning about phylogeny after reading this book.

The Phylogenetic Handbook

A Practical Approach to Phylogenetic

Analysis and Hypothesis Testing (2009)

by

Philippe Lemey

Marco Salemi

Anne-Mieke Vandamme

publisher: Cambridge University Press 

best regards

I think this is an excellent introduction:

Molecular Evolution: A Phylogenetic Approach by Rod Page & Eddie Holmes Blackwell Science

I think Baum and Smith (2013) is very good for starting.

The following book exercices is a well doe introducing matter.  It is available on the webb as a pdf document.

The Compleat Cladist. A primer of Phylogenetic Procédures by E.O. Wiley and al.  1991.

For Cladistic Analysis: Basics of Cladistic Analysis by D. Lipscomb is good at least for basic knowledge.

I see the compleat Cladist. 1991, special publication no.19, The University of Kansas is listed, but  the BASIC key stone,  is

Phylogenetics: the theory and practice of phylogenetic systematics by E.O.Wiley  1981.

Phylonenetics. E.O. Wiley. 1981. Is a good textbook to start the study where you can underestand concepts.Principles of Systematic zoology. E. Mayr & P. Ashlock. 1991. This is a good textbook to know phenetic, cladistic and other methods used in plylogeny.

I think "Wägele, J.W. 2005. Foundations of Phylogenetic Systematics, Pfeil Verlag" is a good introductory book. It starts with a more philosophyical intriduction, for instance covering evolutionary epistemology, recaps some concepts like gene tranfer, before it then covers phylogeny and cladistic methods as such. The language is easy to follow and understand and well suited as an undergraduate introduction.

Also, the book is available as an open-access pdf file at the webpage of the Pfeil Verlag, the publisher of the book: http://www.pfeil-verlag.de/04biol/e3_56.php

Hi!

I think that Molecular Evolution: A Phylogenetic Approach by Rod Page & Eddie Holmes Blackwell Science is a good starting. It was and is very useful to me.

I would recommend "Tree Thinking", by David Baum and S. Smith. 

You may use "Foundations of Phylogenetic Systematics", Johann-Wolfgang Wägele (chapter 6).

The Phylogenetic Handbook edited by Lemey et al. has a good introduction that covers the basics of molecular phylogenetics.

I recomend "The complete cladist", freely available at https://archive.org/details/compleatcladistp00wile

"Phylogenetics: Theory and Practice of Phylogenetic Systematics" thats more or less a 'real' Textbook.

"Phylogenetic Trees Made Easy: A How-to Manual" that's more like a methodological guide book. 

I would go with "Phylogenetic Trees Made Easy: A How-to Manual". Although it is more a methodological manual with a lot of practical examples, some basics are covered and there's an excellent bibliography.

Check this one also: Molecular Evolution and Phylogenetics by Nei & Kumar. This book includes some explanations on what the algorithms are doing.

"Evolution" by Douglass Futuyma, a textbook for undergrads. See the first three chapters.

"Functional and Phylogenetic ecology in R"

If you're looking to get more specific with plant phylogenetics, "Plant Systematics: A Phylogenetic Approach" Judd, Campbell et. al. is a really useful and user friendly resource

The phylogenetic handbook: A practical approach to phylogenetic analysis and hypothesis testing (Lemey, Salemi and Vandamme) is a good one, but you can try too Phylogenetic trees made easy : a how to manual  (Barry G. Hall) which is more practical 

If you aim to understand the theoretical basis of phylogenetics I recommend:

Wiley EO, Lieberman BS (2011) Phylogenetics. Theory and Practice of Phylogenetic Systematics. Wiley & Sons, New York, 432 p.

"The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing" is a very thorough introduction to phylogenetic methods.

I woul recommend:

Hall, Barry G. Phylogenetic trees made easy : a how-to manual / Barry G. Hall. Sunderland, Massachusetts : Sinauer, cop. 2011